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Marasco M, Kirkpatrick J, Carlomagno T, Hub JS, Anselmi M. Phosphopeptide binding to the N-SH2 domain of tyrosine phosphatase SHP2 correlates with the unzipping of its central β-sheet. Comput Struct Biotechnol J 2024; 23:1169-1180. [PMID: 38510972 PMCID: PMC10951427 DOI: 10.1016/j.csbj.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
SHP2 is a tyrosine phosphatase that plays a regulatory role in multiple intracellular signaling cascades and is known to be oncogenic in certain contexts. In the absence of effectors, SHP2 adopts an autoinhibited conformation with its N-SH2 domain blocking the active site. Given the key role of N-SH2 in regulating SHP2, this domain has been extensively studied, often by X-ray crystallography. Using a combination of structural analyses and molecular dynamics (MD) simulations we show that the crystallographic environment can significantly influence the structure of the isolated N-SH2 domain, resulting in misleading interpretations. As an orthogonal method to X-ray crystallography, we use a combination of NMR spectroscopy and MD simulations to accurately determine the conformation of apo N-SH2 in solution. In contrast to earlier reports based on crystallographic data, our results indicate that apo N-SH2 in solution primarily adopts a conformation with a fully zipped central β-sheet, and that partial unzipping of this β-sheet is promoted by binding of either phosphopeptides or even phosphate/sulfate ions.
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Affiliation(s)
- Michelangelo Marasco
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Kirkpatrick
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Teresa Carlomagno
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
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2
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Wang M, Yu K, Fu W, Yang L. The combination of SHP099 inhibits the malignant biological behavior of L-OHP/5-FU-resistant colorectal cancer cells by regulating energy metabolism reprogramming. Biochem Biophys Res Commun 2024; 728:150262. [PMID: 38959530 DOI: 10.1016/j.bbrc.2024.150262] [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: 03/18/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND AND OBJECTIVE Colorectal cancer (CRC) is one of the most common malignancies in China. At present, there is a problem that the CRC treatment drugs SHP099, L-OHP and 5-FU are insensitive to tumor cells. Combination medication is an important means to solve the insensitivity of medication alone. The purpose of this project was to explore the effect and molecular mechanism of SHP099 combination on the malignant biological behavior of L-OHP/5-FU resistant strains of CRC. METHODS HT29 and SW480 cells were cultured in media supplemented with L-OHP or 5-FU to establish drug-resistant strains. HT29 and SW480 drug-resistant cells were subcutaneously injected into the ventral nerves of nude mice at a dose of 5 × 106 to establish CRC drug-resistant animal models. CCK-8, Western blot, flow cytometry, Transwell and kit detection were used to detect the regulatory mechanism of energy metabolism reprogramming in drug-resistant CRC cells. RESULTS Compared with nonresistant strains, L-OHP/5-FU-resistant strains exhibited greater metabolic reprogramming. Functionally, SHP099 can restrain the metabolic reprogramming of L-OHP/5-FU-resistant strains and subsequently restrain the proliferation, colony formation, migration and spheroid formation of L-OHP/5-FU-resistant strains. Downstream mechanistic studies have shown that SHP099 interferes with the metabolic reprogramming of L-OHP/5-FU drug-resistant strains by suppressing the PI3K/AKT pathway, thereby restraining the malignant biological behavior of L-OHP/5-FU drug-resistant strains and alleviating CRC. CONCLUSION The combination of SHP099 can restrain the malignant biological behavior of L-OHP/5-FU-resistant CRC cells and alleviate the progression of CRC by interfering with the reprogramming of energy metabolism. This study explored the effect of SHP099 combination on dual-resistant CRC cells for the first time, and provided a new therapeutic idea for solving the problem of SHP099 insensitivity to CRC cells.
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Affiliation(s)
- Meilian Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Kun Yu
- Department of Colorectal Surgery, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming, 650118, China
| | - Wen Fu
- Department of Gastroenterology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Lihong Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China.
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3
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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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4
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Hossain MA. Targeting the RAS upstream and downstream signaling pathway for cancer treatment. Eur J Pharmacol 2024; 979:176727. [PMID: 38866361 DOI: 10.1016/j.ejphar.2024.176727] [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: 03/08/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
Cancer often involves the overactivation of RAS/RAF/MEK/ERK (MAPK) and PI3K-Akt-mTOR pathways due to mutations in genes like RAS, RAF, PTEN, and PIK3CA. Various strategies are employed to address the overactivation of these pathways, among which targeted therapy emerges as a promising approach. Directly targeting specific proteins, leads to encouraging results in cancer treatment. For instance, RTK inhibitors such as imatinib and afatinib selectively target these receptors, hindering ligand binding and reducing signaling initiation. These inhibitors have shown potent efficacy against Non-Small Cell Lung Cancer. Other inhibitors, like lonafarnib targeting Farnesyltransferase and GGTI 2418 targeting geranylgeranyl Transferase, disrupt post-translational modifications of proteins. Additionally, inhibition of proteins like SOS, SH2 domain, and Ras demonstrate promising anti-tumor activity both in vivo and in vitro. Targeting downstream components with RAF inhibitors such as vemurafenib, dabrafenib, and sorafenib, along with MEK inhibitors like trametinib and binimetinib, has shown promising outcomes in treating cancers with BRAF-V600E mutations, including myeloma, colorectal, and thyroid cancers. Furthermore, inhibitors of PI3K (e.g., apitolisib, copanlisib), AKT (e.g., ipatasertib, perifosine), and mTOR (e.g., sirolimus, temsirolimus) exhibit promising efficacy against various cancers such as Invasive Breast Cancer, Lymphoma, Neoplasms, and Hematological malignancies. This review offers an overview of small molecule inhibitors targeting specific proteins within the RAS upstream and downstream signaling pathways in cancer.
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Affiliation(s)
- Md Arafat Hossain
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh.
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5
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Skeens E, Maschietto F, Manjula R, Shillingford S, Lolis EJ, Batista VS, Bennett AM, Lisi GP. Dynamic and structural insights into allosteric regulation on MKP5 a dual-specificity phosphatase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.05.611520. [PMID: 39282375 PMCID: PMC11398491 DOI: 10.1101/2024.09.05.611520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Dual-specificity mitogen-activated protein kinase (MAPK) phosphatases (MKPs) directly dephosphorylate and inactivate the MAPKs. Although the catalytic mechanism of dephosphorylation of the MAPKs by the MKPs is established, a complete molecular picture of the regulatory interplay between the MAPKs and MKPs still remains to be fully explored. Here, we sought to define the molecular mechanism of MKP5 regulation through an allosteric site within its catalytic domain. We demonstrate using crystallographic and NMR spectroscopy approaches that residue Y435 is required to maintain the structural integrity of the allosteric pocket. Along with molecular dynamics simulations, these data provide insight into how changes in the allosteric pocket propagate conformational flexibility in the surrounding loops to reorganize catalytically crucial residues in the active site. Furthermore, Y435 contributes to the interaction with p38 MAPK and JNK, thereby promoting dephosphorylation. Collectively, these results highlight the role of Y435 in the allosteric site as a novel mode of MKP5 regulation by p38 MAPK and JNK.
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Affiliation(s)
- Erin Skeens
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | | | - Ramu Manjula
- Department of Pharmacology, Yale School of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Shanelle Shillingford
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Department of Pharmacology, Yale School of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Elias J Lolis
- Department of Pharmacology, Yale School of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Anton M Bennett
- Department of Pharmacology, Yale School of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, Connecticut, USA
| | - George P Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
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6
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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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7
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Ou X, Gao G, Habaz IA, Wang Y. Mechanisms of resistance to tyrosine kinase inhibitor-targeted therapy and overcoming strategies. MedComm (Beijing) 2024; 5:e694. [PMID: 39184861 PMCID: PMC11344283 DOI: 10.1002/mco2.694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 07/24/2024] [Accepted: 07/28/2024] [Indexed: 08/27/2024] Open
Abstract
Tyrosine kinase inhibitor (TKI)-targeted therapy has revolutionized cancer treatment by selectively blocking specific signaling pathways crucial for tumor growth, offering improved outcomes with fewer side effects compared with conventional chemotherapy. However, despite their initial effectiveness, resistance to TKIs remains a significant challenge in clinical practice. Understanding the mechanisms underlying TKI resistance is paramount for improving patient outcomes and developing more effective treatment strategies. In this review, we explored various mechanisms contributing to TKI resistance, including on-target mechanisms and off-target mechanisms, as well as changes in the tumor histology and tumor microenvironment (intrinsic mechanisms). Additionally, we summarized current therapeutic approaches aiming at circumventing TKI resistance, including the development of next-generation TKIs and combination therapies. We also discussed emerging strategies such as the use of dual-targeted antibodies and PROteolysis Targeting Chimeras. Furthermore, we explored future directions in TKI-targeted therapy, including the methods for detecting and monitoring drug resistance during treatment, identification of novel targets, exploration of dual-acting kinase inhibitors, application of nanotechnologies in targeted therapy, and so on. Overall, this review provides a comprehensive overview of the challenges and opportunities in TKI-targeted therapy, aiming to advance our understanding of resistance mechanisms and guide the development of more effective therapeutic approaches in cancer treatment.
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Affiliation(s)
- Xuejin Ou
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China HospitalSichuan UniversityChengduChina
| | - Ge Gao
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China HospitalSichuan UniversityChengduChina
- Clinical Trial Center, National Medical Products Administration Key Laboratory for Clinical Research and Evaluation of Innovative Drugs, West China HospitalSichuan UniversityChengduChina
| | - Inbar A. Habaz
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonOntarioCanada
| | - Yongsheng Wang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China HospitalSichuan UniversityChengduChina
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8
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Li W, Mei W, Jiang H, Wang J, Li X, Quan L, Diao Y, Ma Y, Fan S, Xie Z, Gong M, Zhu H, Bi D, Zhang F, Ma L, Zhang J, Gao Y, Paschalidis A, Lin H, Liu F, Liu K, Ye M, Zhao Z, Duan Y, Chen Z, Xu Y, Xiao W, Tao S, Zhu L, Li H. Blocking the PD-1 signal transduction by occupying the phosphorylated ITSM recognition site of SHP-2. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2706-2. [PMID: 39235560 DOI: 10.1007/s11427-024-2706-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 08/07/2024] [Indexed: 09/06/2024]
Abstract
Targeting the PD-1/PD-L1 axis with small-molecular inhibitors is a promising approach for immunotherapy. Here, we identify a natural pentacyclic triterpenoid, Pygenic Acid A (PA), as a PD-1 signaling inhibitor. PA exerts anti-tumor activity in hPD-1 knock-in C57BL/6 mice and enhances effector functions of T cells to promote immune responses by disrupting the PD-1 signaling transduction. Furthermore, we identify SHP-2 as the direct molecular target of PA for inhibiting the PD-1 signaling transduction. Subsequently, mechanistic studies suggest that PA binds to a new druggable site in the phosphorylated PD-1 ITSM recognition site of SHP-2, inhibiting the recruitment of SHP-2 by PD-1. Taken together, our findings demonstrate that PA has a potential application in cancer immunotherapy and occupying the phosphorylated ITSM recognition site of SHP-2 may serve as an alternative strategy to develop PD-1 signaling inhibitors. In addition, our success in target recognition provides a paradigm of target identification and confirmation for natural products.
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Affiliation(s)
- Wenjie Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Wenyi Mei
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Hewei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
- Lingang Laboratory, Shanghai, 200031, China
| | - Jie Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Xiaoli Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Lina Quan
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Yanyan Diao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Yanni Ma
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Sisi Fan
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Zhuwei Xie
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Mengdie Gong
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Huan Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Dewen Bi
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Feng Zhang
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Lei Ma
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Jian Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Yufeng Gao
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Aris Paschalidis
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Fangfang Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Science, College of Medicine, Zhengzhou University, Zhengzhou, 450001, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Science, College of Medicine, Zhengzhou University, Zhengzhou, 450001, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Yajun Duan
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zhuo Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Yufang Xu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Weilie Xiao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China.
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China.
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China.
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China.
- Lingang Laboratory, Shanghai, 200031, China.
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9
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Ma C, Kang D, Gao P, Zhang W, Wu X, Xu Z, Han H, Zhang L, Cai Y, Wang Y, Wang Y, Long W. Discovery of JAB-3312, a Potent SHP2 Allosteric Inhibitor for Cancer Treatment. J Med Chem 2024; 67:13534-13549. [PMID: 39110625 DOI: 10.1021/acs.jmedchem.4c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
As an oncogenic phosphatase, SHP2 acts as a converging node in the RTK-RAS-MAPK signaling pathway in cancer cells and suppresses antitumor immunity by passing signals downstream of PD-1. Here, we utilized the extra druggable pocket outside the previously identified SHP2 allosteric tunnel site by the (6,5 fused), 6 spirocyclic system. The optimized compound, JAB-3312, exhibited a SHP2 binding Kd of 0.37 nM, SHP2 enzymatic IC50 of 1.9 nM, KYSE-520 antiproliferative IC50 of 7.4 nM and p-ERK inhibitory IC50 of 0.23 nM. For JAB-3312, an oral dose of 1.0 mg/kg QD was sufficient to achieve 95% TGI in KYSE-520 xenograft model of mouse. JAB-3312 was well-tolerated in animal models, and a close correlation was observed between the plasma concentration of JAB-3312 and the p-ERK inhibition in tumors. Currently, JAB-3312 is undergoing clinical trials as a potential anticancer agent.
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Affiliation(s)
- Cunbo Ma
- Medicinal Chemistry, Jacobio Pharmaceuticals, Beijing 101111, China
| | - Di Kang
- Pharmacology, Jacobio Pharmaceuticals, Beijing 101111, China
| | - Panliang Gao
- Medicinal Chemistry, Jacobio Pharmaceuticals, Beijing 101111, China
| | - Wei Zhang
- Hits Discovery, Jacobio Pharmaceuticals, Beijing 101111, China
| | - Xinping Wu
- Medicinal Chemistry, Jacobio Pharmaceuticals, Beijing 101111, China
| | - Zilong Xu
- Medicinal Chemistry, Jacobio Pharmaceuticals, Beijing 101111, China
| | - Huifeng Han
- Pharmacology, Jacobio Pharmaceuticals, Beijing 101111, China
| | - Lei Zhang
- Pharmacology, Jacobio Pharmaceuticals, Beijing 101111, China
| | - Yang Cai
- Pharmacology, Jacobio Pharmaceuticals, Beijing 101111, China
| | - Yanping Wang
- Pharmacology, Jacobio Pharmaceuticals, Beijing 101111, China
| | - Yinxiang Wang
- Pharmacology, Jacobio Pharmaceuticals, Beijing 101111, China
| | - Wei Long
- Medicinal Chemistry, Jacobio Pharmaceuticals, Beijing 101111, China
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10
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Perdikari A, Woods VA, Ebrahim A, Lawler K, Bounds R, Singh NI, Mehlman T(S, Riley BT, Sharma S, Morris JW, Keogh JM, Henning E, Smith M, Farooqi IS, Keedy DA. Structures of human PTP1B variants reveal allosteric sites to target for weight loss therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.603709. [PMID: 39149290 PMCID: PMC11326154 DOI: 10.1101/2024.08.05.603709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Protein Tyrosine Phosphatase 1B (PTP1B) is a negative regulator of leptin signaling whose disruption protects against diet-induced obesity in mice. We investigated whether structural characterization of human PTP1B variant proteins might reveal precise mechanisms to target for weight loss therapy. We selected 12 rare variants for functional characterization from exomes from 997 people with persistent thinness and 200,000 people from UK Biobank. Seven of 12 variants impaired PTP1B function by increasing leptin-stimulated STAT3 phosphorylation in cells. Using room-temperature X-ray crystallography, hydrogen-deuterium exchange mass spectrometry, and computational modeling, we determined that human variants modulate the 3-dimensional structure of PTP1B through distinct allosteric conduits that energetically link distal, highly ligandable structural regions to the active site. These studies inform the design of allosteric PTP1B inhibitors for the treatment of obesity.
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Affiliation(s)
- Aliki Perdikari
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Virgil A. Woods
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center; New York, NY 10016, USA
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Katherine Lawler
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Rebecca Bounds
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Nathanael I. Singh
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Tamar (Skaist) Mehlman
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center; New York, NY 10016, USA
| | - Blake T. Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Shivani Sharma
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
- PhD Program in Biology, CUNY Graduate Center; New York, NY 10016, USA
| | - Jackson W. Morris
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Julia M. Keogh
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Elana Henning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Miriam Smith
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - I. Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
- Department of Chemistry and Biochemistry, City College of New York; New York, NY 10031, USA
- PhD Programs in Biochemistry, Biology, and Chemistry, CUNY Graduate Center; New York, NY 10016, USA
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11
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Shi X, Gekas C, Verduzco D, Petiwala S, Jeffries C, Lu C, Murphy E, Anton T, Vo AH, Xiao Z, Narayanan P, Sun BC, D'Souza AL, Barnes JM, Roy S, Ramathal C, Flister MJ, Dezso Z. Building a translational cancer dependency map for The Cancer Genome Atlas. NATURE CANCER 2024; 5:1176-1194. [PMID: 39009815 PMCID: PMC11358024 DOI: 10.1038/s43018-024-00789-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/31/2024] [Indexed: 07/17/2024]
Abstract
Cancer dependency maps have accelerated the discovery of tumor vulnerabilities that can be exploited as drug targets when translatable to patients. The Cancer Genome Atlas (TCGA) is a compendium of 'maps' detailing the genetic, epigenetic and molecular changes that occur during the pathogenesis of cancer, yet it lacks a dependency map to translate gene essentiality in patient tumors. Here, we used machine learning to build translational dependency maps for patient tumors, which identified tumor vulnerabilities that predict drug responses and disease outcomes. A similar approach was used to map gene tolerability in healthy tissues to prioritize tumor vulnerabilities with the best therapeutic windows. A subset of patient-translatable synthetic lethalities were experimentally tested, including PAPSS1/PAPSS12 and CNOT7/CNOT78, which were validated in vitro and in vivo. Notably, PAPSS1 synthetic lethality was driven by collateral deletion of PAPSS2 with PTEN and was correlated with patient survival. Finally, the translational dependency map is provided as a web-based application for exploring tumor vulnerabilities.
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Affiliation(s)
- Xu Shi
- AbbVie Bay Area, South San Francisco, CA, USA
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12
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Tang K, Wang S, Feng S, Yang X, Guo Y, Ren X, Bai L, Yu B, Liu HM, Song Y. Discovery of TK-642 as a highly potent, selective, orally bioavailable pyrazolopyrazine-based allosteric SHP2 inhibitor. Acta Pharm Sin B 2024; 14:3624-3642. [PMID: 39234614 PMCID: PMC11372460 DOI: 10.1016/j.apsb.2024.03.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/20/2024] [Accepted: 03/14/2024] [Indexed: 09/06/2024] Open
Abstract
Src homology-2-containing protein tyrosine phosphatase 2 (SHP2) is a promising therapeutic target for cancer therapy. In this work, we presented the structure-guided design of 5,6-fused bicyclic allosteric SHP2 inhibitors, leading to the identification of pyrazolopyrazine-based TK-642 as a highly potent, selective, orally bioavailable allosteric SHP2 inhibitor (SHP2WT IC50 = 2.7 nmol/L) with favorable pharmacokinetic profiles (F = 42.5%; t 1/2 = 2.47 h). Both dual inhibition biochemical assay and docking analysis indicated that TK-642 likely bound to the "tunnel" allosteric site of SHP2. TK-642 could effectively suppress cell proliferation (KYSE-520 cells IC50 = 5.73 μmol/L) and induce apoptosis in esophageal cancer cells by targeting the SHP2-mediated AKT and ERK signaling pathways. Additionally, oral administration of TK-642 also demonstrated effective anti-tumor effects in the KYSE-520 xenograft mouse model, with a T/C value of 83.69%. Collectively, TK-642 may warrant further investigation as a promising lead compound for the treatment of esophageal cancer.
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Affiliation(s)
- Kai Tang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Shu Wang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Siqi Feng
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Xinyu Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Yueyang Guo
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Xiangli Ren
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Linyue Bai
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- College of Chemistry, Pingyuan Laboratory, State Key Laboratory of Antiviral Drugs, Zhengzhou University, Zhengzhou 450001, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou 450000, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Yihui Song
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
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13
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Wang A, Zhang Y, Lv X, Liang G. Therapeutic potential of targeting protein tyrosine phosphatases in liver diseases. Acta Pharm Sin B 2024; 14:3295-3311. [PMID: 39220870 PMCID: PMC11365412 DOI: 10.1016/j.apsb.2024.05.006] [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: 03/18/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 09/04/2024] Open
Abstract
Protein tyrosine phosphorylation is a post-translational modification that regulates protein structure to modulate demic organisms' homeostasis and function. This physiological process is regulated by two enzyme families, protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). As an important regulator of protein function, PTPs are indispensable for maintaining cell intrinsic physiology in different systems, as well as liver physiological and pathological processes. Dysregulation of PTPs has been implicated in multiple liver-related diseases, including chronic liver diseases (CLDs), hepatocellular carcinoma (HCC), and liver injury, and several PTPs are being studied as drug therapeutic targets. Therefore, given the regulatory role of PTPs in diverse liver diseases, a collated review of their function and mechanism is necessary. Moreover, based on the current research status of targeted therapy, we emphasize the inclusion of several PTP members that are clinically significant in the development and progression of liver diseases. As an emerging breakthrough direction in the treatment of liver diseases, this review summarizes the research status of PTP-targeting compounds in liver diseases to illustrate their potential in clinical treatment. Overall, this review aims to support the development of novel PTP-based treatment pathways for liver diseases.
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Affiliation(s)
- Ao Wang
- Department of Pharmacy and Institute of Inflammation, Zhejiang Provincial Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji 133002, China
| | - Yi Zhang
- Department of Pharmacy and Institute of Inflammation, Zhejiang Provincial Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, China
| | - Xinting Lv
- Department of Pharmacy and Institute of Inflammation, Zhejiang Provincial Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, China
| | - Guang Liang
- Department of Pharmacy and Institute of Inflammation, Zhejiang Provincial Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji 133002, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
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14
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Xiang H, Bai L, Zhang X, Dan T, Cheng P, Yang X, Ai H, Li K, Lei X. A facile strategy for the construction of a phage display cyclic peptide library for the selection of functional macrocycles. Chem Sci 2024; 15:11847-11855. [PMID: 39092106 PMCID: PMC11290325 DOI: 10.1039/d4sc03207a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/16/2024] [Indexed: 08/04/2024] Open
Abstract
Cyclic peptides represent invaluable scaffolds in biological affinity, providing diverse collections for discovering functional molecules targeting challenging biological entities and protein-protein interactions. The field increasingly focuses on developing cyclization strategies and chemically modified combinatorial libraries in conjunction with M13 phage display, to identify macrocyclic peptide inhibitors for traditionally challenging targets. Here, we introduce a cyclization strategy utilizing ortho-phthalaldehyde (OPA) for the discovery of active macrocycles characterized by asymmetric scaffolds with side-chain cyclization. Through this approach, aldehyde groups attached to free molecules sequentially attack the ε-amine of lysine and the thiol of cysteine, facilitating the rapid cyclization of genetically encoded linear precursor libraries displayed on phage particles. The construction of a 109-member library and subsequent screening successfully identified cyclic peptide binders targeting three therapeutically relevant proteins: PTP1B, NEK7, and hKeap1. The results confirm the efficacy in rapidly obtaining active ligands with micromolar potency. This work provides a fast and efficient operable high-throughput platform for screening functional peptide macrocycles, which hold promise for broad application in therapeutics, chemically biological probes, and disease diagnosis.
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Affiliation(s)
- Hua Xiang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Liwen Bai
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Xindan Zhang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Ting Dan
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Peng Cheng
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Xiaoqin Yang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou Magnetic Resonance Center, College of Chemistry and Chemical Engineering, Lanzhou University Lanzhou 730000 China
| | - Honglian Ai
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
| | - Kai Li
- College of Life Sciences, South-Central Minzu University Wuhan 430074 China
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 China
- State Key Laboratory of Applied Organic Chemistry, Lanzhou Magnetic Resonance Center, College of Chemistry and Chemical Engineering, Lanzhou University Lanzhou 730000 China
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15
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Hoffman M, Krum D, Wittrup KD. Bivalent target-binding bioPROTACs induce potent degradation of oncogenic SHP2. J Biol Chem 2024; 300:107616. [PMID: 39089586 PMCID: PMC11387696 DOI: 10.1016/j.jbc.2024.107616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/02/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Targeted protein degradation is an emergent and rapidly evolving therapeutic strategy. In particular, biologics-based targeted degradation modalities (bioPROTACs) are relatively under explored compared to small molecules. Here, we investigate how target affinity, cellular localization, and valency of bioPROTACs impact efficacy of targeted degradation of the oncogenic phosphatase src-homology 2 containing protein tyrosine phosphatase-2 (SHP2). We identify bivalent recruitment of SHP2 by bioPROTACs as a broadly applicable strategy to improve potency. Moreover, we demonstrate that SHP2-targeted bioPROTACs can effectively counteract gain-of-function SHP2 mutants present in cancer, which are otherwise challenging to selectively target with small molecule constructs. Overall, this study demonstrates the utility of bioPROTACs for challenging targets, and further explicates design principles for therapeutic bioPROTACs.
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Affiliation(s)
- Megan Hoffman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David Krum
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - K Dane Wittrup
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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16
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Zhu C, Zhao H, Yang W, Chen K, Liu X, Yu Y, Li R, Tan R, Yu Z. Design, Synthesis and Antitumor Activity of a Novel Class of SHP2 Allosteric Inhibitors with a Furanyl Amide-Based Scaffold. J Med Chem 2024. [PMID: 39066713 DOI: 10.1021/acs.jmedchem.4c01217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
SHP2 plays a critical role in modulating tumor growth and PD-1-related signaling pathway, thereby serving as an attractive antitumor target. To date, no antitumor drugs targeting SHP2 have been approved, and hence, the search of SHP2 inhibitors with new chemical scaffolds is urgently needed. Herein, we developed a novel SHP2 allosteric inhibitor SDUY038 with a furanyl amide scaffold, demonstrating potent binding affinity (KD = 0.29 μM), enzymatic activity (IC50 = 1.2 μM) and similar binding interactions to SHP099. At the cellular level, SDUY038 exhibited pan-antitumor activity (IC50 = 7-24 μM) by suppressing pERK expression. Furthermore, SDUY038 significantly inhibited tumor growth in both xenograft and organoid models. Additionally, SDUY038 displayed acceptable bioavailability (F = 14%) and half-life time (t1/2 = 3.95 h). Conclusively, this study introduces the furanyl amide scaffold as a novel class of SHP2 allosteric inhibitors, offering promising lead compounds for further development of new antitumor therapies targeting SHP2.
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Affiliation(s)
- Chengchun Zhu
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, P.R. China
| | - Haiyang Zhao
- School of Life Science and Engineering, Southwest University of Science and Technology, No. 59, Middle Section of Qinglong Avenue, Mianyang 621010, P.R. China
- Center for Organoids and Translational Pharmacology, Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Institute for Translational Chinese Medicine, Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, P.R. China
| | - Wenting Yang
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, P.R. China
| | - Kai Chen
- Center for New Drug Evaluation, Shandong Academy of Pharmaceutical Sciences, Jinan 250000, P.R. China
| | - Xiaoyu Liu
- Center for New Drug Evaluation, Shandong Academy of Pharmaceutical Sciences, Jinan 250000, P.R. China
| | - Yan Yu
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, P.R. China
| | - Rui Li
- Sichuan Cancer Hospital and Institute, School of Medicine, University of Electronic Science and Technology of China, No. 55, Section 4, South Renmin Road, Chengdu 610041, P.R. China
| | - Ruirong Tan
- Center for Organoids and Translational Pharmacology, Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Institute for Translational Chinese Medicine, Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, P.R. China
| | - Zhiyi Yu
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, P.R. China
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17
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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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18
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Liu B, Zhou H, Tan L, Siu KTH, Guan XY. Exploring treatment options in cancer: Tumor treatment strategies. Signal Transduct Target Ther 2024; 9:175. [PMID: 39013849 PMCID: PMC11252281 DOI: 10.1038/s41392-024-01856-7] [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: 01/23/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 07/18/2024] Open
Abstract
Traditional therapeutic approaches such as chemotherapy and radiation therapy have burdened cancer patients with onerous physical and psychological challenges. Encouragingly, the landscape of tumor treatment has undergone a comprehensive and remarkable transformation. Emerging as fervently pursued modalities are small molecule targeted agents, antibody-drug conjugates (ADCs), cell-based therapies, and gene therapy. These cutting-edge treatment modalities not only afford personalized and precise tumor targeting, but also provide patients with enhanced therapeutic comfort and the potential to impede disease progression. Nonetheless, it is acknowledged that these therapeutic strategies still harbour untapped potential for further advancement. Gaining a comprehensive understanding of the merits and limitations of these treatment modalities holds the promise of offering novel perspectives for clinical practice and foundational research endeavours. In this review, we discussed the different treatment modalities, including small molecule targeted drugs, peptide drugs, antibody drugs, cell therapy, and gene therapy. It will provide a detailed explanation of each method, addressing their status of development, clinical challenges, and potential solutions. The aim is to assist clinicians and researchers in gaining a deeper understanding of these diverse treatment options, enabling them to carry out effective treatment and advance their research more efficiently.
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Affiliation(s)
- Beilei Liu
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China
| | - Hongyu Zhou
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
| | - Licheng Tan
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
| | - Kin To Hugo Siu
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
| | - Xin-Yuan Guan
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China.
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China.
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China.
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China.
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19
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Fan H, Hu X, Cao F, Zhou L, Wen R, Shen H, Fu Y, Zhu X, Jia H, Liu Z, Wang G, Yu G, Chang W, Zhang W. WWP1 inhibition increases SHP2 inhibitor efficacy in colorectal cancer. NPJ Precis Oncol 2024; 8:144. [PMID: 39014007 PMCID: PMC11252267 DOI: 10.1038/s41698-024-00650-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024] Open
Abstract
Protein tyrosine phosphatase SHP2 activates RAS signaling, which is a novel target for colorectal cancer (CRC) therapy. However, SHP2 inhibitor monotherapy is ineffective for metastatic CRC and a combination therapy is required. In this study, we aimed to improve the antitumor efficacy of SHP2 inhibition and try to explore the resistance mechanism of SHP2 inhibitor. Results showed that WWP1 promoted the proliferation of CRC cells. Genetic or pharmacological inhibition of WWP1 enhanced the effect of SHP2 inhibitor in suppressing tumor growth in vitro and in vivo. WWP1 may mediate feedback reactivation of AKT signaling following SHP2 inhibition. Furthermore, nomogram models constructed with IHC expression of WWP1 and SHP2 greatly improved the accuracy of prognosis prediction for patients with CRC. Our findings indicate that WWP1 inhibitor I3C can synergize with SHP2 inhibitor and is expected to be a new strategy for clinical trials in treating advanced CRC patients.
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Affiliation(s)
- Hao Fan
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xuefei Hu
- Department of Navy Environmental and Occupational Health, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Fuao Cao
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Leqi Zhou
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Rongbo Wen
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Hao Shen
- Department of Navy Environmental and Occupational Health, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yating Fu
- Department of Navy Environmental and Occupational Health, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Xiaoming Zhu
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Hang Jia
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Zixuan Liu
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Guimin Wang
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Guanyu Yu
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China.
| | - Wenjun Chang
- Department of Navy Environmental and Occupational Health, Faculty of Naval Medicine, Naval Medical University, Shanghai, China.
| | - Wei Zhang
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China.
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20
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Singh P, Kumar V, Lee KW, Hong JC. Discovery of Novel Allosteric SHP2 Inhibitor Using Pharmacophore-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation, and Principal Component Analysis. Pharmaceuticals (Basel) 2024; 17:935. [PMID: 39065785 PMCID: PMC11280062 DOI: 10.3390/ph17070935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
SHP2 belongs to a cytoplasmic non-receptor protein tyrosine phosphatase class. It plays a critical role in the development of various cancers, such as gastric cancer, leukemia, and breast cancer. Thus, SHP2 has gained the interest of researchers as a potential target for inhibiting tumor cell proliferation in SHP2-dependent cancers. This study employed pharmacophore-based virtual screening, molecular docking, molecular dynamic (MD) simulations, MM/PBSA, and principal component analysis (PCA), followed by ADME prediction. We selected three potential hits from a collective database of more than one million chemical compounds. The stability of these selected hit-protein complexes was analyzed using 500 ns MD simulations and binding free energy calculations. The identified hits Lig_1, Lig_6, and Lig_14 demonstrated binding free energies of -161.49 kJ/mol, -151.28 kJ/mol, and -107.13 kJ/mol, respectively, compared to the reference molecule (SHP099) with a ΔG of -71.48 kJ/mol. Our results showed that the identified compounds could be used as promising candidates for selective SHP2 allosteric inhibition in cancer.
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Affiliation(s)
- Pooja Singh
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea;
| | - Vikas Kumar
- Computational Biophysics Lab, Basque Center for Materials, Applications, and Nanostructures (BCMaterials), Buil. Martina Casiano, Pl. 3 Parque Científico UPV/EHU Barrio Sarriena, 48940 Leioa, Spain;
| | - Keun Woo Lee
- Korea Quantum Computing (KQC), 55 Centumjungang-ro, Haeundae, Busan 48058, Republic of Korea
- Angel i-Drug Design (AiDD), 33-3 Jinyangho-ro 44, Jinju 52650, Republic of Korea
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea;
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21
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Chouhan S, Sridaran D, Weimholt C, Luo J, Li T, Hodgson MC, Santos LN, Le Sommer S, Fang B, Koomen JM, Seeliger M, Qu CK, Yart A, Kontaridis MI, Mahajan K, Mahajan NP. SHP2 as a primordial epigenetic enzyme expunges histone H3 pTyr-54 to amend androgen receptor homeostasis. Nat Commun 2024; 15:5629. [PMID: 38965223 PMCID: PMC11224269 DOI: 10.1038/s41467-024-49978-4] [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: 04/05/2023] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Mutations that decrease or increase the activity of the tyrosine phosphatase, SHP2 (encoded by PTPN11), promotes developmental disorders and several malignancies by varying phosphatase activity. We uncovered that SHP2 is a distinct class of an epigenetic enzyme; upon phosphorylation by the kinase ACK1/TNK2, pSHP2 was escorted by androgen receptor (AR) to chromatin, erasing hitherto unidentified pY54-H3 (phosphorylation of histones H3 at Tyr54) epigenetic marks to trigger a transcriptional program of AR. Noonan Syndrome with Multiple Lentigines (NSML) patients, SHP2 knock-in mice, and ACK1 knockout mice presented dramatic increase in pY54-H3, leading to loss of AR transcriptome. In contrast, prostate tumors with high pSHP2 and pACK1 activity exhibited progressive downregulation of pY54-H3 levels and higher AR expression that correlated with disease severity. Overall, pSHP2/pY54-H3 signaling acts as a sentinel of AR homeostasis, explaining not only growth retardation, genital abnormalities and infertility among NSML patients, but also significant AR upregulation in prostate cancer patients.
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Affiliation(s)
- Surbhi Chouhan
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Dhivya Sridaran
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Cody Weimholt
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Jingqin Luo
- Division of Public Health Sciences, Washington University in St Louis, St Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Tiandao Li
- Bioinformatics Research Core, Center of Regenerative Medicine, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Myles C Hodgson
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
| | - Luana N Santos
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
| | - Samantha Le Sommer
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
| | - Bin Fang
- Moffitt Cancer Center, SRB3, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - John M Koomen
- Moffitt Cancer Center, SRB3, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Markus Seeliger
- Department of Pharmacological Sciences, Stony Brook University Medical School, BST 7-120, Stony Brook, NY, 11794-8651, USA
| | - Cheng-Kui Qu
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Winship Cancer Institute, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Armelle Yart
- UMR 1301-Inserm 5070-CNRS EFS Univ. P. Sabatier, 4bis Ave Hubert Curien, 31100, Toulouse, France
| | - Maria I Kontaridis
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kiran Mahajan
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Nupam P Mahajan
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA.
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, 63110, USA.
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22
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Tang Y, Pu X, Yuan X, Pang Z, Li F, Wang X. Targeting KRASG12D mutation in non-small cell lung cancer: molecular mechanisms and therapeutic potential. Cancer Gene Ther 2024; 31:961-969. [PMID: 38734764 PMCID: PMC11257988 DOI: 10.1038/s41417-024-00778-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/22/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Lung malignant tumors are a type of cancer with high incidence and mortality rates worldwide. Non-small cell lung cancer (NSCLC) accounts for over 80% of all lung malignant tumors, and most patients are diagnosed at advanced stages, leading to poor prognosis. Over the past decades, various oncogenic driver alterations associated with lung cancer have been identified, each of which can potentially serve as a therapeutic target. Rat sarcoma (RAS) genes are the most commonly mutated oncogenes in human cancers, with Kirsten rat sarcoma (KRAS) being the most common subtype. The role of KRAS oncogene in NSCLC is still not fully understood, and its impact on prognosis remains controversial. Despite the significant advancements in targeted therapy and immune checkpoint inhibitors (ICI) that have transformed the treatment landscape of advanced NSCLC in recent years, targeting KRAS (both directly and indirectly) remains challenging and is still under intensive research. In recent years, significant progress has been made in the development of targeted drugs targeting the NSCLC KRASG12C mutant subtype. However, research progress on target drugs for the more common KRASG12D subtype has been slow, and currently, no specific drugs have been approved for clinical use, and many questions remain to be answered, such as the mechanisms of resistance in this subtype of NSCLC, how to better utilize combination strategies with multiple treatment modalities, and whether KRASG12D inhibitors offer substantial efficacy in the treatment of advanced NSCLC patients.
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Affiliation(s)
- Yining Tang
- Department of Radiation Oncology, Cancer Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, 212000, Jiangsu, China
| | - Xi Pu
- Department of Radiation Oncology, Cancer Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, 212000, Jiangsu, China
| | - Xiao Yuan
- Department of Radiation Oncology, Cancer Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, 212000, Jiangsu, China
| | - Zhonghao Pang
- Department of Thoracic Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, 212000, Jiangsu, China
| | - Feng Li
- Department of Thoracic Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, 212000, Jiangsu, China.
| | - Xu Wang
- Department of Radiation Oncology, Cancer Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, 212000, Jiangsu, China.
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23
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Zhou Y, Yao Z, Lin Y, Zhang H. From Tyrosine Kinases to Tyrosine Phosphatases: New Therapeutic Targets in Cancers and Beyond. Pharmaceutics 2024; 16:888. [PMID: 39065585 PMCID: PMC11279542 DOI: 10.3390/pharmaceutics16070888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) regulate the level of tyrosine phosphorylation in proteins. PTKs are key enzymes that catalyze the transfer of an ATP phosphoric acid to a tyrosine residue on target protein substrates. Protein tyrosine phosphatases (PTPs) are responsible for the dephosphorylation of tyrosine residues and play a role in countering PTK overactivity. As widespread oncogenes, PTKs were once considered to be promising targets for therapy. However, tyrosine kinase inhibitors (TKIs) now face a number of challenges, including drug resistance and toxic side effects. Treatment strategies now need to be developed from a new perspective. In this review, we assess the current state of TKIs and highlight the role of PTPs in cancer and other diseases. With the advances of allosteric inhibition and the development of multiple alternative proprietary drug strategies, the reputation of PTPs as "undruggable" targets has been overturned, and they are now considered viable therapeutic targets. We also discuss the strategies and prospects of PTP-targeted therapy, as well as its future development.
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Affiliation(s)
- Yu Zhou
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
| | - Zhimeng Yao
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
- Department of Urology Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510660, China
| | - Yusheng Lin
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
- Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510660, China
| | - Hao Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
- Department of Pathology, Gongli Hospital of Shanghai Pudong New Area, Shanghai 200135, China
- Zhuhai Institute of Jinan University, Zhuhai 511436, China
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24
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Schreiber SL. Molecular glues and bifunctional compounds: Therapeutic modalities based on induced proximity. Cell Chem Biol 2024; 31:1050-1063. [PMID: 38861986 DOI: 10.1016/j.chembiol.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024]
Abstract
This Perspective explores molecular glues and bifunctional compounds-proximity-inducing compounds-and offers a framework to understand and exploit their similarity to hotspots, missense mutations, and posttranslational modifications (PTMs). This view is also shown to be relevant to intramolecular glues, where compounds induce contacts between distinct domains of the same protein. A historical perspective of these compounds is presented that shows the field has come full circle from molecular glues targeting native proteins, to bifunctionals targeting fusion proteins, and back to molecular glues and bifunctionals targeting native proteins. Modern screening methods and data analyses with pre-selected target proteins are shown to yield either cooperative molecular glues or bifunctional compounds that induce proximity, thereby enabling novel functional outcomes.
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Affiliation(s)
- Stuart L Schreiber
- Arena BioWorks, Broad Institute, Harvard University, Cambridge, MA, USA.
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25
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Dong J, Jassim BA, Milholland KL, Qu Z, Bai Y, Miao Y, Miao J, Ma Y, Lin J, Hall MC, Zhang ZY. Development of Novel Phosphonodifluoromethyl-Containing Phosphotyrosine Mimetics and a First-In-Class, Potent, Selective, and Bioavailable Inhibitor of Human CDC14 Phosphatases. J Med Chem 2024; 67:8817-8835. [PMID: 38768084 DOI: 10.1021/acs.jmedchem.4c00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Together with protein tyrosine kinases, protein tyrosine phosphatases (PTPs) control protein tyrosine phosphorylation and regulate numerous cellular functions. Dysregulated PTP activity is associated with the onset of multiple human diseases. Nevertheless, understanding of the physiological function and disease biology of most PTPs remains limited, largely due to the lack of PTP-specific chemical probes. In this study, starting from a well-known nonhydrolyzable phosphotyrosine (pTyr) mimetic, phosphonodifluoromethyl phenylalanine (F2Pmp), we synthesized 7 novel phosphonodifluoromethyl-containing bicyclic/tricyclic aryl derivatives with improved cell permeability and potency toward various PTPs. Furthermore, with fragment- and structure-based design strategies, we advanced compound 9 to compound 15, a first-in-class, potent, selective, and bioavailable inhibitor of human CDC14A and B phosphatases. This study demonstrates the applicability of the fragment-based design strategy in creating potent, selective, and bioavailable PTP inhibitors and provides a valuable probe for interrogating the biological roles of hCDC14 phosphatases and assessing their potential for therapeutic interventions.
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Affiliation(s)
- Jiajun Dong
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brenson A Jassim
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kedric L Milholland
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yunpeng Bai
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yiming Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jinmin Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yuan Ma
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jianping Lin
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhong-Yin Zhang
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
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26
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Miao Y, Bai Y, Miao J, Murray AA, Lin J, Dong J, Qu Z, Zhang RY, Nguyen QD, Wang S, Yu J, Nguele Meke F, Zhang ZY. Off-target autophagy inhibition by SHP2 allosteric inhibitors contributes to their antitumor activity in RAS-driven cancers. J Clin Invest 2024; 134:e177142. [PMID: 38842946 PMCID: PMC11291269 DOI: 10.1172/jci177142] [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: 10/31/2023] [Accepted: 06/04/2024] [Indexed: 08/02/2024] Open
Abstract
Aberrant activation of RAS/MAPK signaling is common in cancer, and efforts to inhibit pathway components have yielded drugs with promising clinical activities. Unfortunately, treatment-provoked adaptive resistance mechanisms inevitably develop, limiting their therapeutic potential. As a central node essential for receptor tyrosine kinase-mediated RAS activation, SHP2 has emerged as an attractive cancer target. Consequently, many SHP2 allosteric inhibitors are now in clinical testing. Here we discovered a previously unrecognized off-target effect associated with SHP2 allosteric inhibitors. We found that these inhibitors accumulate in the lysosome and block autophagic flux in an SHP2-independent manner. We showed that off-target autophagy inhibition by SHP2 allosteric inhibitors contributes to their antitumor activity. We also demonstrated that SHP2 allosteric inhibitors harboring this off-target activity not only suppress oncogenic RAS signaling but also overcome drug resistance such as MAPK rebound and protective autophagy in response to RAS/MAPK pathway blockage. Finally, we exemplified a therapeutic framework that harnesses both the on- and off-target activities of SHP2 allosteric inhibitors for improved treatment of mutant RAS-driven and drug-resistant malignancies such as pancreatic and colorectal cancers.
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Affiliation(s)
- Yiming Miao
- Department of Medicinal Chemistry and Molecular Pharmacology and
| | - Yunpeng Bai
- Department of Medicinal Chemistry and Molecular Pharmacology and
| | - Jinmin Miao
- Department of Medicinal Chemistry and Molecular Pharmacology and
| | | | - Jianping Lin
- Department of Medicinal Chemistry and Molecular Pharmacology and
| | - Jiajun Dong
- Department of Medicinal Chemistry and Molecular Pharmacology and
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Ruo-Yu Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology and
| | - Quyen D. Nguyen
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Shaomeng Wang
- Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Jingmei Yu
- Department of Medicinal Chemistry and Molecular Pharmacology and
| | | | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology and
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
- Institute for Cancer Research and
- Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, USA
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27
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Rehman AU, Zhao C, Wu Y, Zhu Q, Luo R. Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy. Int J Mol Sci 2024; 25:6201. [PMID: 38892388 PMCID: PMC11172685 DOI: 10.3390/ijms25116201] [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: 04/17/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression of various human cancers and neurodevelopmental disorders. Allosteric inhibitors have been proposed to regulate its autoinhibition. However, oncogenic mutations, such as E76K, convert SHP2 into its open state, wherein the catalytic cleft becomes fully exposed to its ligands. This study elucidates the dynamic properties of SHP2 structures across different states, with a focus on the effects of oncogenic mutation on two known binding sites of allosteric inhibitors. Through extensive modeling and simulations, we further identified an alternative allosteric binding pocket in solution structures. Additional analysis provides insights into the dynamics and stability of the potential site. In addition, multi-tier screening was deployed to identify potential binders targeting the potential site. Our efforts to identify a new allosteric site contribute to community-wide initiatives developing therapies using multiple allosteric inhibitors to target distinct pockets on SHP2, in the hope of potentially inhibiting or slowing tumor growth associated with SHP2.
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Affiliation(s)
| | | | | | | | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, CA 92697, USA; (A.U.R.)
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28
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Pandey G, Mazzacurati L, Rowsell TM, Horvat NP, Amin NE, Zhang G, Akuffo AA, Colin-Leitzinger CM, Haura EB, Kuykendall AT, Zhang L, Epling-Burnette PK, Reuther GW. SHP2 inhibition displays efficacy as a monotherapy and in combination with JAK2 inhibition in preclinical models of myeloproliferative neoplasms. Am J Hematol 2024; 99:1040-1055. [PMID: 38440831 PMCID: PMC11096011 DOI: 10.1002/ajh.27282] [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: 09/26/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024]
Abstract
Myeloproliferative neoplasms (MPNs), including polycythemia vera, essential thrombocytosis, and primary myelofibrosis, are clonal hematopoietic neoplasms driven by mutationally activated signaling by the JAK2 tyrosine kinase. Although JAK2 inhibitors can improve MPN patients' quality of life, they do not induce complete remission as disease-driving cells persistently survive therapy. ERK activation has been highlighted as contributing to JAK2 inhibitor persistent cell survival. As ERK is a component of signaling by activated RAS proteins and by JAK2 activation, we sought to inhibit RAS activation to enhance responses to JAK2 inhibition in preclinical MPN models. We found the SHP2 inhibitor RMC-4550 significantly enhanced growth inhibition of MPN cell lines in combination with the JAK2 inhibitor ruxolitinib, effectively preventing ruxolitinib persistent growth, and the growth and viability of established ruxolitinib persistent cells remained sensitive to SHP2 inhibition. Both SHP2 and JAK2 inhibition diminished cellular RAS-GTP levels, and their concomitant inhibition enhanced ERK inactivation and increased apoptosis. Inhibition of SHP2 inhibited the neoplastic growth of MPN patient hematopoietic progenitor cells and exhibited synergy with ruxolitinib. RMC-4550 antagonized MPN phenotypes and increased survival of an MPN mouse model driven by MPL-W515L. The combination of RMC-4550 and ruxolitinib, which was safe and tolerated in healthy mice, further inhibited disease compared to ruxolitinib monotherapy, including extending survival. Given SHP2 inhibitors are undergoing clinical evaluation in patients with solid tumors, our preclinical findings suggest that SHP2 is a candidate therapeutic target with potential for rapid translation to clinical assessment to improve current targeted therapies for MPN patients.
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Affiliation(s)
- Garima Pandey
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL USA
| | - Lucia Mazzacurati
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL USA
| | - Tegan M. Rowsell
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL USA
| | | | - Narmin E. Amin
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL USA
| | - Guolin Zhang
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, FL USA
| | - Afua A. Akuffo
- Department of Immunology, Moffitt Cancer Center, Tampa, FL USA
| | | | - Eric B. Haura
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, FL USA
| | | | - Ling Zhang
- Department of Pathology, Moffitt Cancer Center, Tampa, FL USA
| | | | - Gary W. Reuther
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL USA
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL USA
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29
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Zhao M, Shuai W, Su Z, Xu P, Wang A, Sun Q, Wang G. Protein tyrosine phosphatases: emerging role in cancer therapy resistance. Cancer Commun (Lond) 2024; 44:637-653. [PMID: 38741380 PMCID: PMC11194456 DOI: 10.1002/cac2.12548] [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: 10/31/2023] [Revised: 04/14/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Tyrosine phosphorylation of intracellular proteins is a post-translational modification that plays a regulatory role in signal transduction during cellular events. Dephosphorylation of signal transduction proteins caused by protein tyrosine phosphatases (PTPs) contributed their role as a convergent node to mediate cross-talk between signaling pathways. In the context of cancer, PTP-mediated pathways have been identified as signaling hubs that enabled cancer cells to mitigate stress induced by clinical therapy. This is achieved by the promotion of constitutive activation of growth-stimulatory signaling pathways or modulation of the immune-suppressive tumor microenvironment. Preclinical evidences suggested that anticancer drugs will release their greatest therapeutic potency when combined with PTP inhibitors, reversing drug resistance that was responsible for clinical failures during cancer therapy. AREAS COVERED This review aimed to elaborate recent insights that supported the involvement of PTP-mediated pathways in the development of resistance to targeted therapy and immune-checkpoint therapy. EXPERT OPINION This review proposed the notion of PTP inhibition in anticancer combination therapy as a potential strategy in clinic to achieve long-term tumor regression. Ongoing clinical trials are currently underway to assess the safety and efficacy of combination therapy in advanced-stage tumors.
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Affiliation(s)
- Min Zhao
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Wen Shuai
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Zehao Su
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
- West China Biomedical Big Data CenterMed‐X Center for InformaticsSichuan UniversityChengduSichuanP. R. China
| | - Ping Xu
- Emergency DepartmentZigong Fourth People's HospitalChengduSichuanP. R. China
| | - Aoxue Wang
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Qiu Sun
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Guan Wang
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
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30
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Na B, Shah SR, Vasudevan HN. Past, Present, and Future Therapeutic Strategies for NF-1-Associated Tumors. Curr Oncol Rep 2024; 26:706-713. [PMID: 38709422 PMCID: PMC11169015 DOI: 10.1007/s11912-024-01527-4] [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] [Accepted: 03/27/2024] [Indexed: 05/07/2024]
Abstract
PURPOSE OF REVIEW Neurofibromatosis type 1 (NF-1) is a cancer predisposition syndrome caused by mutations in the NF1 tumor suppressor gene that encodes the neurofibromin protein, which functions as a negative regulator of Ras signaling. We review the past, current, and future state of therapeutic strategies for tumors associated with NF-1. RECENT FINDINGS Therapeutic efforts for NF-1-associated tumors have centered around inhibiting Ras output, leading to the clinical success of downstream MEK inhibition for plexiform neurofibromas and low-grade gliomas. However, MEK inhibition and similar molecular monotherapy approaches that block Ras signaling do not work for all patients and show limited efficacy for more aggressive cancers such as malignant peripheral nerve sheath tumors and high-grade gliomas, motivating novel treatment approaches. We highlight the current therapeutic landscape for NF-1-associated tumors, broadly categorizing treatment into past strategies for serial Ras pathway blockade, current approaches targeting parallel oncogenic and tumor suppressor pathways, and future avenues of investigation leveraging biologic and technical innovations in immunotherapy, pharmacology, and gene delivery.
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Affiliation(s)
- Brian Na
- Department of Neurology, UCLA Neuro-Oncology Program, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Shilp R Shah
- Samueli School of Engineering, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA.
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31
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Hsu MF, Koike S, Chen CS, Najjar SM, Meng TC, Haj FG. Pharmacological inhibition of the Src homology phosphatase 2 confers partial protection in a mouse model of alcohol-associated liver disease. Biomed Pharmacother 2024; 175:116590. [PMID: 38653109 DOI: 10.1016/j.biopha.2024.116590] [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: 09/26/2023] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Alcohol-associated liver disease (ALD) is a leading factor of liver-related death worldwide. ALD has various manifestations that include steatosis, hepatitis, and cirrhosis and is currently without approved pharmacotherapies. The Src homology phosphatase 2 (Shp2) is a drug target in some cancers due to its positive regulation of Ras-mitogen-activated protein kinase signaling and cell proliferation. Shp2 pharmacological inhibition yields beneficial outcomes in animal disease models, but its impact on ALD remains unexplored. This study aims to investigate the effects of Shp2 inhibition and its validity using a preclinical mouse model of ALD. We report that the administration of SHP099, a potent and selective allosteric inhibitor of Shp2, partially ameliorated ethanol-induced hepatic injury, inflammation, and steatosis in mice. Additionally, Shp2 inhibition was associated with reduced ethanol-evoked activation of extracellular signal-regulated kinase (ERK), oxidative, and endoplasmic reticulum (ER) stress in the liver. Besides the liver, excessive alcohol consumption induces multi-organ injury and dysfunction, including the intestine. Notably, Shp2 inhibition diminished ethanol-induced intestinal inflammation and permeability, abrogated the reduction in tight junction protein expression, and the activation of ERK and stress signaling in the ileum. Collectively, Shp2 pharmacological inhibition mitigates the deleterious effects of ethanol in the liver and intestine in a mouse model of ALD. Given the multifactorial aspects underlying ALD pathogenesis, additional studies are needed to decipher the utility of Shp2 inhibition alone or as a component in a multitherapeutic regimen to combat this deadly malady.
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Affiliation(s)
- Ming-Fo Hsu
- Department of Nutrition, University of California Davis, One Shields Ave, Davis, CA 95616, USA.
| | - Shinichiro Koike
- Department of Nutrition, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Chang-Shan Chen
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan
| | - Sonia M Najjar
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA; Diabetes Institute, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Tzu-Ching Meng
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan
| | - Fawaz G Haj
- Department of Nutrition, University of California Davis, One Shields Ave, Davis, CA 95616, USA; Comprehensive Cancer Center, University of California Davis, Sacramento, CA 95817, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, University of California Davis, Sacramento, CA 95817, USA.
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32
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Liu Y, Jang H, Nussinov R. SHP2-EGFR States in Dephosphorylation Can Inform Selective SHP2 Inhibitors, Dampening RasGAP Action. J Phys Chem B 2024; 128:5175-5187. [PMID: 38747619 DOI: 10.1021/acs.jpcb.4c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
SHP2 is a positive regulator of the EGFR-dependent Ras/MAPK pathway. It dephosphorylates a regulatory phosphorylation site in EGFR that serves as the binding site to RasGAP (RASA1 or p120RasGAP). RASA1 is activated by binding to the EGFR phosphate group. Active RASA1 deactivates Ras by hydrolyzing Ras-bound GTP to GDP. Thus, SHP2 dephosphorylation of EGFR effectively prevents RASA1-mediated deactivation of Ras, thereby stimulating proliferation. Despite knowledge of this vital regulation in cell life, mechanistic in-depth structural understanding of the involvement of SHP2, EGFR, and RASA1 in the Ras/MAPK pathway has largely remained elusive. Here we elucidate the interactions, the factors influencing EGFR's recruitment of RASA1, and SHP2's recognition of the substrate site in EGFR. We reveal that RASA1 specifically interacts with the DEpY992LIP motif in EGFR featuring a proline residue at the +3 position C-terminal to pY primarily through its nSH2 domain. This interaction is strengthened by the robust attraction of two acidic residues, E991 and D990, of EGFR to two basic residues in the BC-loop near the pY-binding pocket of RASA1's nSH2. In the stable precatalytic state of SHP2 with EGFR (DADEpY992LIPQ), the E-loop of SHP2's active site favors the interaction with the (-2)-position D990 and (-4)-position D988 N-terminal to pY992 in EGFR, while the pY-loop constrains the (+4)-position Q996 C-terminal to pY992. These specific interactions not only provide a structural basis for identifying negative regulatory sites in other RTKs but can inform selective, high-affinity active-site SHP2 inhibitors tailored for SHP2 mutants.
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Affiliation(s)
- Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Yang L, Zhao H, Yuan F, Chen M, Ma N, Yin Z, Liu H, Guo Y. Computational study on the binding mechanism of allosteric drug TNO155 inhibiting SHP2 E76A. Mol Divers 2024:10.1007/s11030-024-10881-1. [PMID: 38807000 DOI: 10.1007/s11030-024-10881-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/15/2024] [Indexed: 05/30/2024]
Abstract
E76A mutations of SHP2 have been reported to associate with genetic developmental diseases and cancers, and TNO155 is one of the effective inhibitors targeted to the allosteric site 1, which has already entered the clinical stage. However, the detailed binding mechanism between them still needs further clarification at micro-atomic level. In this study, the binding mechanism of TNO155 inhibiting SHP2E76A and the superiorities of TNO155 at binding affinity and dynamic interactive behavior with SHP2E76A were probed utilizing a series of computational drug design technologies. The results show that SHP2E76A forms tighter interaction with TNO155 compared to SHP099. SHP2E76A-TNO155 exhibits the largest electrostatic interaction among all complex systems, which can be manifested by the strong hydrogen bond interactions formed by two electrically charged residues, Arg111 and Glu250. Notably, in SHP2E76A-TNO155 system, Asp489 makes an additional substantial beneficial contribution. The E76A mutation brings stronger residue positive correlation and a larger conformation fluctuation between N-CH2 and PTP domains, resulting in tighter binding between TNO155 and SHP2E76A. This study offers valuable insights for the further design and development of novel SHP2E76A allosteric inhibitors.
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Affiliation(s)
- Longhua Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Huijian Zhao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Fanru Yuan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Mengguo Chen
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Nannan Ma
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zhili Yin
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Hongmin Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Henan Province for Drug Quality and Evaluation, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou, 450001, China
| | - Yong Guo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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Han X, Wang W, Wang R, Zhang W, Zhu L, Xu Q, Guo W, Gu Y. Allosteric SHP2 inhibition enhances regorafenib's effectiveness in colorectal cancer treatment. Biochem Biophys Res Commun 2024; 709:149812. [PMID: 38564942 DOI: 10.1016/j.bbrc.2024.149812] [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: 01/09/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
Colorectal cancer (CRC) is the third most common cancer globally. Regorafenib, a multi-target kinase inhibitor, has been approved for treating metastatic colorectal cancer patients who have undergone at least two prior standard anti-cancer therapies. However, regorafenib efficacy as a single agent remains suboptimal. A promising target at the crossroads of multiple signaling pathways is the Src homology 2 domain-containing protein tyrosine phosphatase (SHP2). However, a combination approach using SHP2 inhibitors (SHP099) and anti-angiogenic drugs (Regorafenib) has not been reported in current research. In this study, we conducted in vitro experiments combining SHP099 and regorafenib and established an MC-38 colon cancer allograft mouse model. Our results revealed that co-treatment with SHP099 and regorafenib significantly inhibited cell viability and altered the biological characteristics of tumor cells compared with treatment alone in vitro. Furthermore, the combination strategy demonstrated superior therapeutic efficacy compared to monotherapy with either drug. This was evidenced by reduced tumor size, decreased proliferation, increased apoptosis, normalized tumor microvasculature, and improved antitumor immune response in vivo. These findings suggest that the combination of an SHP2 inhibitor and regorafenib is a promising therapeutic approach for patients with colorectal cancer.
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Affiliation(s)
- Xiao Han
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Weicheng Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Zhang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China; Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Lijun Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
| | - Wenjie Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
| | - Yanhong Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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35
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Zhou Y, Tao L, Qiu J, Xu J, Yang X, Zhang Y, Tian X, Guan X, Cen X, Zhao Y. Tumor biomarkers for diagnosis, prognosis and targeted therapy. Signal Transduct Target Ther 2024; 9:132. [PMID: 38763973 PMCID: PMC11102923 DOI: 10.1038/s41392-024-01823-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 03/07/2024] [Accepted: 04/02/2024] [Indexed: 05/21/2024] Open
Abstract
Tumor biomarkers, the substances which are produced by tumors or the body's responses to tumors during tumorigenesis and progression, have been demonstrated to possess critical and encouraging value in screening and early diagnosis, prognosis prediction, recurrence detection, and therapeutic efficacy monitoring of cancers. Over the past decades, continuous progress has been made in exploring and discovering novel, sensitive, specific, and accurate tumor biomarkers, which has significantly promoted personalized medicine and improved the outcomes of cancer patients, especially advances in molecular biology technologies developed for the detection of tumor biomarkers. Herein, we summarize the discovery and development of tumor biomarkers, including the history of tumor biomarkers, the conventional and innovative technologies used for biomarker discovery and detection, the classification of tumor biomarkers based on tissue origins, and the application of tumor biomarkers in clinical cancer management. In particular, we highlight the recent advancements in biomarker-based anticancer-targeted therapies which are emerging as breakthroughs and promising cancer therapeutic strategies. We also discuss limitations and challenges that need to be addressed and provide insights and perspectives to turn challenges into opportunities in this field. Collectively, the discovery and application of multiple tumor biomarkers emphasized in this review may provide guidance on improved precision medicine, broaden horizons in future research directions, and expedite the clinical classification of cancer patients according to their molecular biomarkers rather than organs of origin.
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Affiliation(s)
- Yue Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lei Tao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiahao Qiu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Xu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinyu Yang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yu Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- School of Medicine, Tibet University, Lhasa, 850000, China
| | - Xinyu Tian
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinqi Guan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaobo Cen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yinglan Zhao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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36
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Eghdami S, Afrashteh F, Shojaii A, Abolhasani M, Motevalian M. The therapeutic effect of alcoholic extract of Fumaria parviflora on high-fat diet-induced nonalcoholic fatty liver in rats: an animal experiment. Ann Med Surg (Lond) 2024; 86:2657-2664. [PMID: 38694306 PMCID: PMC11060231 DOI: 10.1097/ms9.0000000000001890] [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: 01/25/2024] [Accepted: 02/21/2024] [Indexed: 05/04/2024] Open
Abstract
Background and purpose Nonalcoholic fatty liver disease (NAFLD) is a growing problem with a significant burden. Lifestyle modification is the recommended treatment, but researchers are exploring other options. This study focused on the effects of Fumaria parviflora (FP) extracts on NAFLD induced by a high-fat diet in rats. Experimental approach Thirty-five 10-week-old male Wister-Albino rats were divided into seven groups: normal diet control, high fat diet control, high fat diet with oral normal saline gavage, high fat diet with oral Atorvastatin gavage, and three groups receiving high fat diet with FP extract in 200 mg/kg, 400 mg/kg, and 700 mg/kg.Blood samples of rats were used for the measurement of total cholesterol (TC), low-density lipoprotein (LDL), high-density lipoprotein (HDL), triglyceride (TG), alanine aminotransferase (ALT), aspartate aminotransferase (AST) and alkaline phosphatase (ALP).1×1 cm Liver biopsies were taken, stained with Trichrome Stain (Masson) and Hematoxylin and eosin (H&E) stain for evaluation by a pathologist. Findings/results Lab results showed that FP extract inhibits weight gain, has positive effects on triglyceride and alkaline phosphatase levels, and reduces hepatocyte ballooning and inflammation in rats. Conclusion FP extract may lower liver enzymes and have a positive impact on triglyceride, LDL, and HDL levels in rats with NAFLD.
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Affiliation(s)
- Shayan Eghdami
- Pharmacology Department, School of Medicine, Iran University of Medical Sciences
- Cellular and Molecular Research Center, Iran University of Medical Sciences
| | - Fatemeh Afrashteh
- Pharmacology Department, School of Medicine, Iran University of Medical Sciences
- Student Research Committee, School of Medicine, Iran University of Medical Sciences
| | - Asie Shojaii
- Student Research Committee, School of Medicine, Iran University of Medical Sciences
- Institute for Studies in Medical History, Persian and Complementary Medicine, Iran University of Medical Sciences
| | - Maryam Abolhasani
- Department of Traditional Pharmacy, School of Persian Medicine, Iran University of Medical Sciences
| | - Manijeh Motevalian
- Pharmacology Department, School of Medicine, Iran University of Medical Sciences
- Department of Pathology, School of Medicine, Oncopathology Research Center, Hasheminejad Kidney Center, Iran University of Medical Sciences
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran
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Lee S, Kim J, Ryu HH, Jang H, Lee D, Lee S, Song JM, Lee YS, Ho Suh Y. SHP2 regulates GluA2 tyrosine phosphorylation required for AMPA receptor endocytosis and mGluR-LTD. Proc Natl Acad Sci U S A 2024; 121:e2316819121. [PMID: 38657042 PMCID: PMC11066993 DOI: 10.1073/pnas.2316819121] [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: 10/02/2023] [Accepted: 03/29/2024] [Indexed: 04/26/2024] Open
Abstract
Posttranslational modifications regulate the properties and abundance of synaptic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors that mediate fast excitatory synaptic transmission and synaptic plasticity in the central nervous system. During long-term depression (LTD), protein tyrosine phosphatases (PTPs) dephosphorylate tyrosine residues in the C-terminal tail of AMPA receptor GluA2 subunit, which is essential for GluA2 endocytosis and group I metabotropic glutamate receptor (mGluR)-dependent LTD. However, as a selective downstream effector of mGluRs, the mGluR-dependent PTP responsible for GluA2 tyrosine dephosphorylation remains elusive at Schaffer collateral (SC)-CA1 synapses. In the present study, we find that mGluR5 stimulation activates Src homology 2 (SH2) domain-containing phosphatase 2 (SHP2) by increasing phospho-Y542 levels in SHP2. Under steady-state conditions, SHP2 plays a protective role in stabilizing phospho-Y869 of GluA2 by directly interacting with GluA2 phosphorylated at Y869, without affecting GluA2 phospho-Y876 levels. Upon mGluR5 stimulation, SHP2 dephosphorylates GluA2 at Y869 and Y876, resulting in GluA2 endocytosis and mGluR-LTD. Our results establish SHP2 as a downstream effector of mGluR5 and indicate a dual action of SHP2 in regulating GluA2 tyrosine phosphorylation and function. Given the implications of mGluR5 and SHP2 in synaptic pathophysiology, we propose SHP2 as a promising therapeutic target for neurodevelopmental and autism spectrum disorders.
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Affiliation(s)
- Sanghyeon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul03080, South Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
- Transplantation Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
| | - Jungho Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul03080, South Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
- Transplantation Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
| | - Hyun-Hee Ryu
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul03080, South Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul03080, South Korea
| | - Hanbyul Jang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul03080, South Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul03080, South Korea
| | - DoEun Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul03080, South Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
- Transplantation Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
| | - Seungha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul03080, South Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
- Transplantation Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
| | - Jae-man Song
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul03080, South Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
- Transplantation Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
| | - Yong-Seok Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul03080, South Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul03080, South Korea
| | - Young Ho Suh
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul03080, South Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
- Transplantation Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul03080, South Korea
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Gao Y, Xing S, Hu L. Probing the Immunoreceptor Tyrosine-Based Inhibition Motif Interaction Protein Partners with Proteomics. Molecules 2024; 29:1977. [PMID: 38731468 PMCID: PMC11085718 DOI: 10.3390/molecules29091977] [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: 03/20/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Phosphorylation of tyrosine is the basic mode of protein function and signal transduction in organisms. This process is regulated by protein tyrosine kinases (PTKs) and protein tyrosinases (PTPs). Immunoreceptor tyrosine-based inhibition motif (ITIM) has been considered as regulating the PTP activity through the interaction with the partner proteins in the cell signal pathway. The ITIM sequences need to be phosphorylated first to active the downstream signaling proteins. To explore potential regulatory mechanisms, the ITIM sequences of two transmembrane immunoglobulin proteins, myelin P0 protein-related protein (PZR) and programmed death 1 (PD-1), were analyzed to investigate their interaction with proteins involved in regulatory pathways. We discovered that phosphorylated ITIM sequences can selectively interact with the tyrosine phosphatase SHP2. Specifically, PZR-N-ITIM (pY) may be critical in the interaction between the ITIM and SH2 domains of SHP2, while PD1-C-ITSM (pY) may play a key role in the interaction between the ITIM and SH2 domains of SHP2. Quite a few proteins were identified containing the SH2 domain, exhibiting phosphorylation-mediated interaction with PZR-ITIM. In this study, 14 proteins with SH2 structural domains were identified by GO analysis on 339 proteins associated to the affinity pull-down of PZR-N-ITIM (pY). Through the SH2 domains, these proteins may interact with PZR-ITIM in a phosphorylation-dependent manner.
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Affiliation(s)
| | - Shu Xing
- School of Life Sciences, Jilin University, Changchun 130012, China;
| | - Lianghai Hu
- School of Life Sciences, Jilin University, Changchun 130012, China;
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39
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Hall A, Chatzopoulou M, Frost J. Bioisoteres for carboxylic acids: From ionized isosteres to novel unionized replacements. Bioorg Med Chem 2024; 104:117653. [PMID: 38579492 DOI: 10.1016/j.bmc.2024.117653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 04/07/2024]
Abstract
Carboxylic acids are key pharmacophoric elements in many molecules. They can be seen as a problem by some, due to perceived permeability challenges, potential for high plasma protein binding and the risk of forming reactive metabolites due to acyl-glucuronidation. By others they are viewed more favorably as they can decrease lipophilicity by adding an ionizable center which can be beneficial for solubility, and can add enthalpic interactions with the target protein. However, there are many instances where the replacement of a carboxylic acid with a bioisosteric group is required. This has led to the development of a number of ionizable groups which sufficiently mimic the carboxylic acid functionality whilst improving, for example, the metabolic profile of the molecule in question. An alternative strategy involves replacement of the carboxylate by neutral functional groups. This review initially details carefully selected examples whereby tetrazoles, acyl sulfonamides or isoxazolols have been beneficially utilized as carboxylic acid bioisosteres altering physicohemical properties, interactions with the target and metabolism and/or pharmacokinetics, before delving further into the binding mode of carboxylic acid derivatives with their target proteins. This analysis highlights new ways to consider the replacement of carboxylic acids by neutral bioisosteric groups which either rely on hydrogen bonds or cation-π interactions. It should serve as a useful guide for scientists working in drug discovery.
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Affiliation(s)
- Adrian Hall
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK.
| | - Maria Chatzopoulou
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK
| | - James Frost
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK
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40
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Yuan Z, Zhang M, Chang L, Chen X, Ruan S, Shi S, Zhang Y, Zhu L, Li H, Li S. Discovery of a novel SHP2 allosteric inhibitor using virtual screening, FMO calculation, and molecular dynamic simulation. J Mol Model 2024; 30:131. [PMID: 38613643 DOI: 10.1007/s00894-024-05935-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/09/2024] [Indexed: 04/15/2024]
Abstract
CONTEXT SHP2 is a non-receptor protein tyrosine phosphatase to remove tyrosine phosphorylation. Functionally, SHP2 is an essential bridge to connect numerous oncogenic cell-signaling cascades including RAS-ERK, PI3K-AKT, JAK-STAT, and PD-1/PD-L1 pathways. This study aims to discover novel and potent SHP2 inhibitors using a hierarchical structure-based virtual screening strategy that combines molecular docking and the fragment molecular orbital method (FMO) for calculating binding affinity (referred to as the Dock-FMO protocol). For the SHP2 target, the FMO method prediction has a high correlation between the binding affinity of the protein-ligand interaction and experimental values (R2 = 0.55), demonstrating a significant advantage over the MM/PBSA (R2 = 0.02) and MM/GBSA (R2 = 0.15) methods. Therefore, we employed Dock-FMO virtual screening of ChemDiv database of ∼2,990,000 compounds to identify a novel SHP2 allosteric inhibitor bearing hydroxyimino acetamide scaffold. Experimental validation demonstrated that the new compound (E)-2-(hydroxyimino)-2-phenyl-N-(piperidin-4-ylmethyl)acetamide (7188-0011) effectively inhibited SHP2 in a dose-dependent manner. Molecular dynamics (MD) simulation analysis revealed the binding stability of compound 7188-0011 and the SHP2 protein, along with the key interacting residues in the allosteric binding site. Overall, our work has identified a novel and promising allosteric inhibitor that targets SHP2, providing a new starting point for further optimization to develop more potent inhibitors. METHODS All the molecular docking studies were employed to identify potential leads with Maestro v10.1. The protein-ligand binding affinities of potential leads were further predicted by FMO calculations at MP2/6-31G* level using GAMESS v2020 system. MD simulations were carried out with AmberTools18 by applying the FF14SB force field. MD trajectories were analyzed using VMD v1.9.3. MM/GB(PB)SA binding free energy analysis was carried out with the mmpbsa.py tool of AmberTools18. The docking and MD simulation results were visualized through PyMOL v2.5.0.
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Affiliation(s)
- Zhen Yuan
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Manzhan Zhang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Longfeng Chang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Xingyu Chen
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Shanshan Ruan
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Shanshan Shi
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Yiqing Zhang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China.
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China.
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China.
- Lingang Laboratory, Shanghai, 200031, China.
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China.
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China.
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41
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Eguchi A, Olsen JV. Phosphoproteomic investigation of targets of protein phosphatases in EGFR signaling. Sci Rep 2024; 14:7908. [PMID: 38575675 PMCID: PMC10995159 DOI: 10.1038/s41598-024-58619-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
Receptor tyrosine kinases (RTKs) initiate cellular signaling pathways, which are regulated through a delicate balance of phosphorylation and dephosphorylation events. While many studies of RTKs have focused on downstream-activated kinases catalyzing the site-specific phosphorylation, few studies have focused on the phosphatases carrying out the dephosphorylation. In this study, we analyzed six protein phosphatase networks using chemical inhibitors in context of epidermal growth factor receptor (EGFR) signaling by mass spectrometry-based phosphoproteomics. Specifically, we focused on protein phosphatase 2C (PP2C), involved in attenuating p38-dependent signaling pathways in various cellular responses, and confirmed its effect in regulating p38 activity in EGFR signaling. Furthermore, utilizing a p38 inhibitor, we classified phosphosites whose phosphorylation status depends on PP2C inhibition into p38-dependent and p38-independent sites. This study provides a large-scale dataset of phosphatase-regulation of EGF-responsive phosphorylation sites, which serves as a useful resource to deepen our understanding of EGFR signaling.
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Affiliation(s)
- Akihiro Eguchi
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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42
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Miao J, Zhang ZY. Drugging Protein Tyrosine Phosphatases through Targeted Protein Degradation. ChemMedChem 2024; 19:e202300669. [PMID: 38233347 PMCID: PMC11021144 DOI: 10.1002/cmdc.202300669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/22/2023] [Accepted: 01/17/2024] [Indexed: 01/19/2024]
Abstract
Protein tyrosine phosphatases (PTPs) are an important class of enzymes that regulate protein tyrosine phosphorylation levels of a large variety of proteins in cells. Anomalies in protein tyrosine phosphorylation have been associated with the development of numerous human diseases, leading to a heightened interest in PTPs as promising targets for drug development. However, therapeutic targeting of PTPs has faced skepticism about their druggability. Besides the conventional small molecule inhibitors, proteolysis-targeting chimera (PROTAC) technology offers an alternative approach to target PTPs. PROTAC molecules utilize the ubiquitin-proteasome system to degrade specific proteins and have unique advantages compared with inhibitors: 1) PROTACs are highly efficient and can work at much lower concentrations than that expected based on their biophysical binding affinity; 2) PROTACs may achieve higher selectivity for the targeted protein than that dictated by their binding affinity alone; and 3) PROTACs may engage any region of the target protein in addition to the functional site. This review focuses on the latest advancement in the development of targeted PTP degraders and deliberates on the obstacles and prospective paths of harnessing this technology for therapeutic targeting of the PTPs.
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Affiliation(s)
- Jinmin Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
| | - Zhong-Yin Zhang
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
- Department of Chemistry, 560 Oval Drive, West Lafayette, IN 47907, USA
- Institute for Cancer Research, Purdue University, 201 S. University Street, West Lafayette, IN 47907, USA
- Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
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43
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Ying K, Xin W, Xu Y, Lv D, Zhu H, Li Y, Xu W, Yan C, Li Y, Cheng H, Chen E, Ma G, Zhang X, Ke Y. NanoSHP099-Targeted SHP2 Inhibition Boosts Ly6C low Monocytes/Macrophages Differentiation to Accelerate Thrombolysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308166. [PMID: 38247197 PMCID: PMC10987109 DOI: 10.1002/advs.202308166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/06/2024] [Indexed: 01/23/2024]
Abstract
Tumor-associated thrombus (TAT) accounts for a high proportion of venous thromboembolism. Traditional thrombolysis and anticoagulation methods are not effective due to various complications and contraindications, which can easily lead to patients dying from TAT rather than the tumor itself. These clinical issues demonstrate the need to research diverse pathways for adjuvant thrombolysis in antitumor therapy. Previously, the phenotypic and functional transformation of monocytes/macrophages is widely reported to be involved in intratribal collagen regulation. This study finds that myeloid deficiency of the oncogene SHP2 sensitizes Ly6Clow monocyte/macrophage differentiation and can alleviate thrombus organization by increasing thrombolytic Matrix metalloproteinase (MMP) 2/9 activities. Moreover, pharmacologic inhibition by SHP099, examined in mouse lung metastatic tumor models, reduces tumor and thrombi burden in tumor metastatic lung tissues. Furthermore, SHP099 increases intrathrombus Ly6Clow monocyte/macrophage infiltration and exhibits thrombolytic function at high concentrations. To improve the thrombolytic effect of SHP099, NanoSHP099 is constructed to achieve the specific delivery of SHP099. NanoSHP099 is identified to be simultaneously enriched in tumor and thrombus foci, exerting dual tumor-suppression and thrombolysis effects. NanoSHP099 presents a superior thrombus dissolution effect than that of the same dosage of SHP099 because of the higher Ly6Clow monocyte/macrophage proportion and MMP2/MMP9 collagenolytic activities in organized thrombi.
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Affiliation(s)
- Kejing Ying
- Department of Pulmonary and Critical Care MedicineRegional Medical Center for National Institute of Respiratory DiseasesSir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Wanghao Xin
- Department of Pulmonary and Critical Care MedicineRegional Medical Center for National Institute of Respiratory DiseasesSir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Yiming Xu
- Department of Pulmonary and Critical Care MedicineRegional Medical Center for National Institute of Respiratory DiseasesSir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Dandan Lv
- Department of Pulmonary and Critical Care MedicineRegional Medical Center for National Institute of Respiratory DiseasesSir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Huiqi Zhu
- Department of Pulmonary and Critical Care MedicineRegional Medical Center for National Institute of Respiratory DiseasesSir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Yeping Li
- Department of Pulmonary and Critical Care MedicineRegional Medical Center for National Institute of Respiratory DiseasesSir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Wangting Xu
- Department of RespiratoryFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Department of Pathology and Pathophysiologyand Department of Respiratory Medicine at Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Chao Yan
- Department of Pulmonary and Critical Care MedicineRegional Medical Center for National Institute of Respiratory DiseasesSir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Yiqing Li
- Department of Pathology and PathophysiologyZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Hongqiang Cheng
- Department of Pathology and PathophysiologyZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Enguo Chen
- Department of Pulmonary and Critical Care MedicineRegional Medical Center for National Institute of Respiratory DiseasesSir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Guofeng Ma
- Department of Pulmonary and Critical Care MedicineRegional Medical Center for National Institute of Respiratory DiseasesSir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Xue Zhang
- Department of Pathology and Pathophysiologyand Department of Respiratory Medicine at Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Yuehai Ke
- Department of Pathology and Pathophysiologyand Department of Respiratory Medicine at Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
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44
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Sun H, Bai X, Zhang Y, Gao Y, Dai J, Xing P, Zhu J, Liu R, Wang Z, Li X. Small Molecule SHP2 Inhibitor LXQ-217 Affects Lung Cancer Cell Proliferation in Vitro and in Vivo. Chem Biodivers 2024; 21:e202301610. [PMID: 38379194 DOI: 10.1002/cbdv.202301610] [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: 10/13/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND SHP2 is highly expressed in a variety of cancer and has emerged as a potential target for cancer therapeutic agents. The identification of uncharged pTyr mimics is an important direction for the development of SHP2 orthosteric inhibitors. METHODS Surface plasmon resonance analysis and cellular thermal shift assay were employed to verify the direct binding of LXQ-217 to SHP2. The inhibitory effect of LXQ-217 was characterized by linear Weaver-Burke enzyme kinetic analysis and BIOVIA Discovery Studio. The inhibition of tumor cell proliferation by LXQ-217 was characterized by cell viability assay, colony formation assays and hoechst 33258 staining. The inhibition of lung cancer proliferation in vivo was studied in nude mice after oral administration of LXQ-217. RESULTS An electroneutral bromophenol derivative, LXQ-217, was identified as a competitive SHP2 inhibitor. LXQ-217 induced apoptosis and inhibited growth of human pulmonary epithelial cells by affecting the RAS-ERK and PI3 K-AKT signaling pathways. Long-term oral administration of LXQ-217 significantly inhibited the proliferation ability of lung cancer cells in nude mice. Moreover, mice administered LXQ-217 orally at high doses exhibited no mortality or significant changes in vital signs. CONCLUSIONS Our findings on the uncharged orthosteric inhibitor provide a foundation for further development of a safe and effective anti-lung cancer drug.
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Affiliation(s)
- Hao Sun
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Xiaoyi Bai
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Yiting Zhang
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Yanan Gao
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Jiajia Dai
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, Shandong, China
| | - Pan Xing
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Jiqiang Zhu
- Shandong Linghai Biotechnology Co., Ltd., 250299, Jinan, Shandong, P. R. China
| | - Ruihua Liu
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Zemin Wang
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Xiangqian Li
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, 266237, Qingdao, Shandong, P. R. China
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45
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Chen Y, Liu QP, Xie H, Ding J. From bench to bedside: current development and emerging trend of KRAS-targeted therapy. Acta Pharmacol Sin 2024; 45:686-703. [PMID: 38049578 PMCID: PMC10943119 DOI: 10.1038/s41401-023-01194-4] [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: 07/23/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) is the most frequently mutated oncogene in human cancers with mutations predominantly occurring in codon 12. These mutations disrupt the normal function of KRAS by interfering with GTP hydrolysis and nucleotide exchange activity, making it prone to the GTP-bound active state, thus leading to sustained activation of downstream pathways. Despite decades of research, there has been no progress in the KRAS drug discovery until the groundbreaking discovery of covalently targeting the KRASG12C mutation in 2013, which led to revolutionary changes in KRAS-targeted therapy. So far, two small molecule inhibitors sotorasib and adagrasib targeting KRASG12C have received accelerated approval for the treatment of non-small cell lung cancer (NSCLC) harboring KRASG12C mutations. In recent years, rapid progress has been achieved in the KRAS-targeted therapy field, especially the exploration of KRASG12C covalent inhibitors in other KRASG12C-positive malignancies, novel KRAS inhibitors beyond KRASG12C mutation or pan-KRAS inhibitors, and approaches to indirectly targeting KRAS. In this review, we provide a comprehensive overview of the molecular and mutational characteristics of KRAS and summarize the development and current status of covalent inhibitors targeting the KRASG12C mutation. We also discuss emerging promising KRAS-targeted therapeutic strategies, with a focus on mutation-specific and direct pan-KRAS inhibitors and indirect KRAS inhibitors through targeting the RAS activation-associated proteins Src homology-2 domain-containing phosphatase 2 (SHP2) and son of sevenless homolog 1 (SOS1), and shed light on current challenges and opportunities for drug discovery in this field.
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Affiliation(s)
- Yi Chen
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiu-Pei Liu
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Department of Chemical and Environment Engineering, Science and Engineering Building, The University of Nottingham Ningbo China, Ningbo, 315100, China
| | - Hua Xie
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.
| | - Jian Ding
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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46
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Holguin-Cruz JA, Bui JM, Jha A, Na D, Gsponer J. Widespread alteration of protein autoinhibition in human cancers. Cell Syst 2024; 15:246-263.e7. [PMID: 38366601 DOI: 10.1016/j.cels.2024.01.009] [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: 01/31/2019] [Revised: 06/20/2023] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Autoinhibition is a prevalent allosteric regulatory mechanism in signaling proteins. Reduced autoinhibition underlies the tumorigenic effect of some known cancer drivers, but whether autoinhibition is altered generally in cancer remains elusive. Here, we demonstrate that cancer-associated missense mutations, in-frame insertions/deletions, and fusion breakpoints are enriched within inhibitory allosteric switches (IASs) across all cancer types. Selection for IASs that are recurrently mutated in cancers identifies established and unknown cancer drivers. Recurrent missense mutations in IASs of these drivers are associated with distinct, cancer-specific changes in molecular signaling. For the specific case of PPP3CA, the catalytic subunit of calcineurin, we provide insights into the molecular mechanisms of altered autoinhibition by cancer mutations using biomolecular simulations, and demonstrate that such mutations are associated with transcriptome changes consistent with increased calcineurin signaling. Our integrative study shows that autoinhibition-modulating genetic alterations are positively selected for by cancer cells.
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Affiliation(s)
- Jorge A Holguin-Cruz
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer M Bui
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ashwani Jha
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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47
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Hu X, Li E, Zhou Y, You Q, Jiang Z. Casitas b cell lymphoma‑B (Cbl-b): A new therapeutic avenue for small-molecule immunotherapy. Bioorg Med Chem 2024; 102:117677. [PMID: 38457911 DOI: 10.1016/j.bmc.2024.117677] [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: 01/12/2024] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Immunotherapy has revolutionized the area of cancer treatment. Although most immunotherapies now are antibodies targeting membrane checkpoint molecules, there is an increasing demand for small-molecule drugs that address intracellular pathways. The E3 ubiquitin ligase Casitas B cell lymphoma‑b (Cbl-b) has been regarded as a promising intracellular immunotherapy target. Cbl-b regulates the downstream proteins of multiple membrane receptors and co-receptors, restricting the activation of the innate and adaptive immune system. Recently, Cbl-b inhibitors have been reported with promising effects on immune surveillance activation and anti-tumor efficacy. Several molecules have entered phase Ⅰ clinical trials. In this review, the biological rationale of Cbl-b as a promising target for cancer immunotherapy and the latest research progress of Cbl-b are summarized, with special emphasis on the allosteric small-molecule inhibitors of Cbl-b.
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Affiliation(s)
- Xiuqi Hu
- State Key Laboratory of Natural Medicines, and Jiang Su 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
| | - Erdong Li
- State Key Laboratory of Natural Medicines, and Jiang Su 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
| | - Yangguo Zhou
- State Key Laboratory of Natural Medicines, and Jiang Su 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
| | - Qidong You
- State Key Laboratory of Natural Medicines, and Jiang Su 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.
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines, and Jiang Su 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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48
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Day JEH, Berdini V, Castro J, Chessari G, Davies TG, Day PJ, St Denis JD, Fujiwara H, Fukaya S, Hamlett CCF, Hearn K, Hiscock SD, Holvey RS, Ito S, Kandola N, Kodama Y, Liebeschuetz JW, Martins V, Matsuo K, Mortenson PN, Muench S, Nakatsuru Y, Ochiiwa H, Palmer N, Peakman T, Price A, Reader M, Rees DC, Rich SJ, Shah A, Shibata Y, Smyth T, Twigg DG, Wallis NG, Williams G, Wilsher NE, Woodhead A, Shimamura T, Johnson CN. Fragment-Based Discovery of Allosteric Inhibitors of SH2 Domain-Containing Protein Tyrosine Phosphatase-2 (SHP2). J Med Chem 2024. [PMID: 38462716 DOI: 10.1021/acs.jmedchem.3c02118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The ubiquitously expressed protein tyrosine phosphatase SHP2 is required for signaling downstream of receptor tyrosine kinases (RTKs) and plays a role in regulating many cellular processes. Genetic knockdown and pharmacological inhibition of SHP2 suppresses RAS/MAPK signaling and inhibit the proliferation of RTK-driven cancer cell lines. Here, we describe the first reported fragment-to-lead campaign against SHP2, where X-ray crystallography and biophysical techniques were used to identify fragments binding to multiple sites on SHP2. Structure-guided optimization, including several computational methods, led to the discovery of two structurally distinct series of SHP2 inhibitors binding to the previously reported allosteric tunnel binding site (Tunnel Site). One of these series was advanced to a low-nanomolar lead that inhibited tumor growth when dosed orally to mice bearing HCC827 xenografts. Furthermore, a third series of SHP2 inhibitors was discovered binding to a previously unreported site, lying at the interface of the C-terminal SH2 and catalytic domains.
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Affiliation(s)
- James E H Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Valerio Berdini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Joan Castro
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Thomas G Davies
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Philip J Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Jeffrey D St Denis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Hideto Fujiwara
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Satoshi Fukaya
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | | | - Keisha Hearn
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Steven D Hiscock
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Rhian S Holvey
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Satoru Ito
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Navrohit Kandola
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yasuo Kodama
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - John W Liebeschuetz
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Vanessa Martins
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Kenichi Matsuo
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Sandra Muench
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yoko Nakatsuru
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Hiroaki Ochiiwa
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Nicholas Palmer
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Torren Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Amanda Price
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Michael Reader
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - David C Rees
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Sharna J Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Alpesh Shah
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yoshihiro Shibata
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Tomoko Smyth
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - David G Twigg
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Nicola G Wallis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Glyn Williams
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Nicola E Wilsher
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Andrew Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Tadashi Shimamura
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
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49
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Chen X, Keller SJ, Hafner P, Alrawashdeh AY, Avery TY, Norona J, Zhou J, Ruess DA. Tyrosine phosphatase PTPN11/SHP2 in solid tumors - bull's eye for targeted therapy? Front Immunol 2024; 15:1340726. [PMID: 38504984 PMCID: PMC10948527 DOI: 10.3389/fimmu.2024.1340726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Encoded by PTPN11, the Src-homology 2 domain-containing phosphatase 2 (SHP2) integrates signals from various membrane-bound receptors such as receptor tyrosine kinases (RTKs), cytokine and integrin receptors and thereby promotes cell survival and proliferation. Activating mutations in the PTPN11 gene may trigger signaling pathways leading to the development of hematological malignancies, but are rarely found in solid tumors. Yet, aberrant SHP2 expression or activation has implications in the development, progression and metastasis of many solid tumor entities. SHP2 is involved in multiple signaling cascades, including the RAS-RAF-MEK-ERK-, PI3K-AKT-, JAK-STAT- and PD-L1/PD-1- pathways. Although not mutated, activation or functional requirement of SHP2 appears to play a relevant and context-dependent dichotomous role. This mostly tumor-promoting and infrequently tumor-suppressive role exists in many cancers such as gastrointestinal tumors, pancreatic, liver and lung cancer, gynecological entities, head and neck cancers, prostate cancer, glioblastoma and melanoma. Recent studies have identified SHP2 as a potential biomarker for the prognosis of some solid tumors. Based on promising preclinical work and the advent of orally available allosteric SHP2-inhibitors early clinical trials are currently investigating SHP2-directed approaches in various solid tumors, either as a single agent or in combination regimes. We here provide a brief overview of the molecular functions of SHP2 and collate current knowledge with regard to the significance of SHP2 expression and function in different solid tumor entities, including cells in their microenvironment, immune escape and therapy resistance. In the context of the present landscape of clinical trials with allosteric SHP2-inhibitors we discuss the multitude of opportunities but also limitations of a strategy targeting this non-receptor protein tyrosine phosphatase for treatment of solid tumors.
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Affiliation(s)
- Xun Chen
- Department of General and Visceral Surgery, Center for Surgery, Medical Center University of Freiburg, Freiburg, Germany
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou, China
| | - Steffen Johannes Keller
- Department of General and Visceral Surgery, Center for Surgery, Medical Center University of Freiburg, Freiburg, Germany
| | - Philipp Hafner
- Department of General and Visceral Surgery, Center for Surgery, Medical Center University of Freiburg, Freiburg, Germany
| | - Asma Y. Alrawashdeh
- Department of General and Visceral Surgery, Center for Surgery, Medical Center University of Freiburg, Freiburg, Germany
| | - Thomas Yul Avery
- Department of General and Visceral Surgery, Center for Surgery, Medical Center University of Freiburg, Freiburg, Germany
| | - Johana Norona
- Department of General and Visceral Surgery, Center for Surgery, Medical Center University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jinxue Zhou
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou, China
| | - Dietrich Alexander Ruess
- Department of General and Visceral Surgery, Center for Surgery, Medical Center University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
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50
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Elbatsh AMO, Amin-Mansour A, Haberkorn A, Textor C, Ebel N, Renard E, Koch LM, Groenveld FC, Piquet M, Naumann U, Ruddy DA, Romanet V, Martínez Gómez JM, Shirley MD, Wipfli P, Schnell C, Wartmann M, Rausch M, Jager MJ, Levesque MP, Maira SM, Manchado E. INPP5A phosphatase is a synthetic lethal target in GNAQ and GNA11-mutant melanomas. NATURE CANCER 2024; 5:481-499. [PMID: 38233483 DOI: 10.1038/s43018-023-00710-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
Activating mutations in GNAQ/GNA11 occur in over 90% of uveal melanomas (UMs), the most lethal melanoma subtype; however, targeting these oncogenes has proven challenging and inhibiting their downstream effectors show limited clinical efficacy. Here, we performed genome-scale CRISPR screens along with computational analyses of cancer dependency and gene expression datasets to identify the inositol-metabolizing phosphatase INPP5A as a selective dependency in GNAQ/11-mutant UM cells in vitro and in vivo. Mutant cells intrinsically produce high levels of the second messenger inositol 1,4,5 trisphosphate (IP3) that accumulate upon suppression of INPP5A, resulting in hyperactivation of IP3-receptor signaling, increased cytosolic calcium and p53-dependent apoptosis. Finally, we show that GNAQ/11-mutant UM cells and patients' tumors exhibit elevated levels of IP4, a biomarker of enhanced IP3 production; these high levels are abolished by GNAQ/11 inhibition and correlate with sensitivity to INPP5A depletion. Our findings uncover INPP5A as a synthetic lethal vulnerability and a potential therapeutic target for GNAQ/11-mutant-driven cancers.
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Affiliation(s)
- Ahmed M O Elbatsh
- Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Ali Amin-Mansour
- Oncology, Novartis Institute for Biomedical Research, Cambridge, MA, USA
| | - Anne Haberkorn
- Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Claudia Textor
- PK Sciences, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Nicolas Ebel
- Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Emilie Renard
- Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Lisa M Koch
- Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Femke C Groenveld
- Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Michelle Piquet
- Oncology, Novartis Institute for Biomedical Research, Cambridge, MA, USA
| | - Ulrike Naumann
- Chemical Biology and Therapeutics, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - David A Ruddy
- Oncology, Novartis Institute for Biomedical Research, Cambridge, MA, USA
| | - Vincent Romanet
- Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Julia M Martínez Gómez
- Dermatology Department, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Matthew D Shirley
- Oncology, Novartis Institute for Biomedical Research, Cambridge, MA, USA
| | - Peter Wipfli
- PK Sciences, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Christian Schnell
- Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Markus Wartmann
- Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Martin Rausch
- Chemical Biology and Therapeutics, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Mitchell P Levesque
- Dermatology Department, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Eusebio Manchado
- Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland.
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