1
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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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Guo Z, Duan Y, Sun K, Zheng T, Liu J, Xu S, Xu J. Advances in SHP2 tunnel allosteric inhibitors and bifunctional molecules. Eur J Med Chem 2024; 275:116579. [PMID: 38889611 DOI: 10.1016/j.ejmech.2024.116579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
SHP2 is a non-receptor tyrosine phosphatase encoded by PTPN11, which performs the functions of regulating cell proliferation, differentiation, apoptosis, and survival through removing tyrosine phosphorylation and modulating various signaling pathways. The overexpression of SHP2 or its mutations is related to developmental diseases and several cancers. Numerous allosteric inhibitors with striking inhibitory potency against SHP2 allosteric pockets have recently been identified, and several SHP2 tunnel allosteric inhibitors have been applied in clinical trials to treat cancers. However, based on clinical results, the efficacy of single-agent treatments has been proven to be suboptimal. Most clinical trials involving SHP2 inhibitors have adopted drug combination strategies. This review briefly discusses the research progress on SHP2 allosteric inhibitors and pathway-dependent drug combination strategies for SHP2 in cancer therapy. In addition, we summarize the current bifunctional molecules of SHP2 and elaborate on the design and structural optimization strategies of these bifunctional molecules in detail, offering further direction for the research on novel SHP2 inhibitors.
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Affiliation(s)
- Zhichao Guo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Yiping Duan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Kai Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Tiandong Zheng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Jie Liu
- Department of Organic Chemistry, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
| | - Shengtao Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
| | - Jinyi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
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3
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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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4
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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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5
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Liang X, Ren H, Han F, Liang R, Zhao J, Liu H. The new direction of drug development: Degradation of undruggable targets through targeting chimera technology. Med Res Rev 2024; 44:632-685. [PMID: 37983964 DOI: 10.1002/med.21992] [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: 11/30/2022] [Revised: 06/13/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Imbalances in protein and noncoding RNA levels in vivo lead to the occurrence of many diseases. In addition to the use of small molecule inhibitors and agonists to restore these imbalances, recently emerged targeted degradation technologies provide a new direction for disease treatment. Targeted degradation technology directly degrades target proteins or RNA by utilizing the inherent degradation pathways, thereby eliminating the functions of pathogenic proteins (or RNA) to treat diseases. Compared with traditional therapies, targeted degradation technology which avoids the principle of traditional inhibitor occupation drive, has higher efficiency and selectivity, and widely expands the range of drug targets. It is one of the most promising and hottest areas for future drug development. Herein, we systematically introduced the in vivo degradation systems applied to degrader design: ubiquitin-proteasome system, lysosomal degradation system, and RNA degradation system. We summarized the development progress, structural characteristics, and limitations of novel chimeric design technologies based on different degradation systems. In addition, due to the lack of clear ligand-binding pockets, about 80% of disease-associated proteins cannot be effectively intervened with through traditional therapies. We deeply elucidated how to use targeted degradation technology to discover and design molecules for representative undruggable targets including transcription factors, small GTPases, and phosphatases. Overall, this review provides a comprehensive and systematic overview of targeted degradation technology-related research advances and a new guidance for the chimeric design of undruggable targets.
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Affiliation(s)
- Xuewu Liang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hairu Ren
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Fengyang Han
- School of Pharmacy, Fudan University, Shanghai, China
| | - Renwen Liang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jiayan Zhao
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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6
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Kim SH, Bulos ML, Adams JA, Yun BK, Bishop AC. Single Ion Pair Is Essential for Stabilizing SHP2's Open Conformation. Biochemistry 2024; 63:273-281. [PMID: 38251939 DOI: 10.1021/acs.biochem.3c00609] [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: 01/23/2024]
Abstract
Src-homology-2-domain-containing PTP-2 (SHP2) is a widely expressed signaling enzyme whose misregulation is associated with multiple human pathologies. SHP2's enzymatic activity is controlled by a conformational equilibrium between its autoinhibited ("closed") state and its activated ("open") state. Although SHP2's closed state has been extensively characterized, the putative structure of its open form has only been revealed in the context of a highly activated mutant (E76K), and no systematic studies of the biochemical determinants of SHP2's open-state stabilization have been reported. To identify amino-acid interactions that are critical for stabilizing SHP2's active state, we carried out a mutagenic study of residues that lie at potentially important interdomain interfaces of the open conformation. The open/closed equilibria of the mutants were evaluated, and we identified several interactions that contribute to the stabilization of SHP2's open state. In particular, our findings establish that an ion pair between glutamate 249 on SHP2's PTP domain and arginine 111 on an interdomain loop is the key determinant of SHP2's open-state stabilization. Mutations that disrupt the R111/E249 ion pair substantially shift SHP2's open/closed equilibrium to the closed state, even compared to wild-type SHP2's basal-state equilibrium, which strongly favors the closed state. To the best of our knowledge, the ion-pair variants uncovered in this study are the first known SHP2 mutants in which autoinhibition is augmented with respect to the wild-type protein. Such "hyperinhibited" mutants may provide useful tools for signaling studies that investigate the connections between SHP2 inhibition and the suppression of human disease progression.
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Affiliation(s)
- Sean H Kim
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - Maya L Bulos
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - Jennifer A Adams
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - B Koun Yun
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - Anthony C Bishop
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
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7
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Xu WQ, Qi SZ, Zhao JF, Li LP, Ding CH, Liu WS. Discovery of 1H-pyrazolo[3,4- b]pyrazine derivatives as selective allosteric inhibitor of protein tyrosine phosphatase SHP2 for the treatment of KRAS G12C-mutant non-small cell lung cancer. J Biomol Struct Dyn 2024:1-9. [PMID: 38258435 DOI: 10.1080/07391102.2024.2308771] [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: 08/16/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024]
Abstract
The high expression or mutation of SHP2 can induce cancer, so targeting SHP2 has become a new strategy for cancer treatment. In this study, we used the previously reported SHP2 allosteric inhibitor IACS-13909 as a lead drug for structural derivation and modification, and synthesized three SHP2 inhibitors. Among them, 1H-pyrazolo[3,4-b]pyrazine derivative 4b was a highly selective SHP2 allosteric inhibitor, with an IC50 value of 3.2 nM, and its inhibitory activity was 17.75 times than that of the positive control IACS-13909. The cell proliferation experiment detected that compound 4b would markedly inhibit the proliferation of various cancer cells. Interestingly, compound 4b was highly sensitive to KRASG12C-mutant non-small cell lung cancer NCI-H358 cells, with an IC50 value of 0.58 μM and its antiproliferative activity was 4.79 times than that of IACS-13909. Furthermore, the combination therapy of compound 4b and KRASG12C inhibitor sotorasib would play a strong synergistic effect against NCI-H358 cells. The western blot experiment detected that compound 4b markedly downregulated the phosphorylation levels of ERK and AKT in NCI-H358 cells. Molecular docking study predicted that compound 4b bound to the allosteric site of SHP2 and formed H-bond interactions with key residues Thr108, Glu110, Arg111, and Phe113. In summary, this study aims to provide new ideas for the development of SHP2 allosteric inhibitors for the treatment of KRASG12C mutant non-small cell lung cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wen-Qiang Xu
- Department of Pharmacy, Binzhou Medical University Hospital, Binzhou, Shandong Province, China
| | - Shi-Zhou Qi
- Department of Pharmacy, Binzhou Medical University Hospital, Binzhou, Shandong Province, China
| | - Ji-Feng Zhao
- Shandong Key Laboratory of Medicine and Health (Clinical Applied Pharmacology), Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, China
| | - Li-Peng Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Chuan-Hua Ding
- Shandong Key Laboratory of Medicine and Health (Clinical Applied Pharmacology), Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, China
| | - Wen-Shan Liu
- Shandong Key Laboratory of Medicine and Health (Clinical Applied Pharmacology), Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, China
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8
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Anselmi M, Hub JS. Atomistic ensemble of active SHP2 phosphatase. Commun Biol 2023; 6:1289. [PMID: 38129686 PMCID: PMC10739809 DOI: 10.1038/s42003-023-05682-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
SHP2 phosphatase plays an important role in regulating several intracellular signaling pathways. Pathogenic mutations of SHP2 cause developmental disorders and are linked to hematological malignancies and cancer. SHP2 comprises two tandemly-arranged SH2 domains, a catalytic PTP domain, and a disordered C-terminal tail. Under physiological, non-stimulating conditions, the catalytic site of PTP is occluded by the N-SH2 domain, so that the basal activity of SHP2 is low. Whereas the autoinhibited structure of SHP2 has been known for two decades, its active, open structure still represents a conundrum. Since the oncogenic mutant SHP2E76K almost completely populates the active, open state, this mutant has been extensively studied as a model for activated SHP2. By molecular dynamics simulations and accurate explicit-solvent SAXS curve predictions, we present the heterogeneous atomistic ensemble of constitutively active SHP2E76K in solution, encompassing a set of conformational arrangements and radii of gyration in agreement with experimental SAXS data.
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Affiliation(s)
- Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany.
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany.
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9
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Miao J, Bai Y, Miao Y, Qu Z, Dong J, Zhang RY, Aggarwal D, Jassim BA, Nguyen Q, Zhang ZY. Discovery of a SHP2 Degrader with In Vivo Anti-Tumor Activity. Molecules 2023; 28:6947. [PMID: 37836790 PMCID: PMC10574094 DOI: 10.3390/molecules28196947] [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: 09/04/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Src homology 2 domain-containing phosphatase 2 (SHP2) is an attractive target for cancer therapy due to its multifaceted roles in both tumor and immune cells. Herein, we designed and synthesized a novel series of proteolysis targeting chimeras (PROTACs) using a SHP2 allosteric inhibitor as warhead, with the goal of achieving SHP2 degradation both inside the cell and in vivo. Among these molecules, compound P9 induces efficient degradation of SHP2 (DC50 = 35.2 ± 1.5 nM) in a concentration- and time-dependent manner. Mechanistic investigation illustrates that the P9-mediated SHP2 degradation requires the recruitment of the E3 ligase and is ubiquitination- and proteasome-dependent. P9 shows improved anti-tumor activity in a number of cancer cell lines over its parent allosteric inhibitor. Importantly, administration of P9 leads to a nearly complete tumor regression in a xenograft mouse model, as a result of robust SHP2 depletion and suppression of phospho-ERK1/2 in the tumor. Hence, P9 represents the first SHP2 PROTAC molecule with excellent in vivo efficacy. It is anticipated that P9 could serve not only as a new chemical tool to interrogate SHP2 biology but also as a starting point for the development of novel therapeutics targeting SHP2.
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Affiliation(s)
- Jinmin Miao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (J.M.); (Y.B.); (Y.M.); (J.D.); (R.-Y.Z.); (D.A.); (B.A.J.)
| | - Yunpeng Bai
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (J.M.); (Y.B.); (Y.M.); (J.D.); (R.-Y.Z.); (D.A.); (B.A.J.)
| | - Yiming Miao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (J.M.); (Y.B.); (Y.M.); (J.D.); (R.-Y.Z.); (D.A.); (B.A.J.)
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; (Z.Q.); (Q.N.)
| | - Jiajun Dong
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (J.M.); (Y.B.); (Y.M.); (J.D.); (R.-Y.Z.); (D.A.); (B.A.J.)
| | - Ruo-Yu Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (J.M.); (Y.B.); (Y.M.); (J.D.); (R.-Y.Z.); (D.A.); (B.A.J.)
| | - Devesh Aggarwal
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (J.M.); (Y.B.); (Y.M.); (J.D.); (R.-Y.Z.); (D.A.); (B.A.J.)
| | - Brenson A. Jassim
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (J.M.); (Y.B.); (Y.M.); (J.D.); (R.-Y.Z.); (D.A.); (B.A.J.)
| | - Quyen Nguyen
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; (Z.Q.); (Q.N.)
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (J.M.); (Y.B.); (Y.M.); (J.D.); (R.-Y.Z.); (D.A.); (B.A.J.)
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; (Z.Q.); (Q.N.)
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
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10
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Li Q, Zhou L, Qin S, Huang Z, Li B, Liu R, Yang M, Nice EC, Zhu H, Huang C. Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications. Eur J Med Chem 2023; 257:115447. [PMID: 37229829 DOI: 10.1016/j.ejmech.2023.115447] [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: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.
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Affiliation(s)
- Qiong Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Zhao Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Ruolan Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Mei Yang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, PR China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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11
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Welsh CL, Allen S, Madan LK. Setting sail: Maneuvering SHP2 activity and its effects in cancer. Adv Cancer Res 2023; 160:17-60. [PMID: 37704288 PMCID: PMC10500121 DOI: 10.1016/bs.acr.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Since the discovery of tyrosine phosphorylation being a critical modulator of cancer signaling, proteins regulating phosphotyrosine levels in cells have fast become targets of therapeutic intervention. The nonreceptor protein tyrosine phosphatase (PTP) coded by the PTPN11 gene "SHP2" integrates phosphotyrosine signaling from growth factor receptors into the RAS/RAF/ERK pathway and is centrally positioned in processes regulating cell development and oncogenic transformation. Dysregulation of SHP2 expression or activity is linked to tumorigenesis and developmental defects. Even as a compelling anti-cancer target, SHP2 was considered "undruggable" for a long time owing to its conserved catalytic PTP domain that evaded drug development. Recently, SHP2 has risen from the "undruggable curse" with the discovery of small molecules that manipulate its intrinsic allostery for effective inhibition. SHP2's unique domain arrangement and conformation(s) allow for a truly novel paradigm of inhibitor development relying on skillful targeting of noncatalytic sites on proteins. In this review we summarize the biological functions, signaling properties, structural attributes, allostery and inhibitors of SHP2.
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Affiliation(s)
- Colin L Welsh
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Sarah Allen
- Department of Pediatrics, Darby Children's Research Institute, Medical University of South Carolina, Charleston, SC, United States
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.
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12
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Rios P, Kiani A, Köhn M. Measuring Protein Tyrosine Phosphatase Activity Dependent on SH2 Domain-Mediated Regulation. Methods Mol Biol 2023; 2705:351-358. [PMID: 37668983 DOI: 10.1007/978-1-0716-3393-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Src-homology-2 (SH2) domains bind selectively to phosphotyrosine (pTyr) residues located in target binding proteins; therefore, they are key elements in pTyr-mediated signaling pathways. The binding of an SH2 domain to a pTyr acts as a docking mechanism that attracts proteins into signaling hubs, and in some cases, it can also regulate the catalytic activity of signaling enzymes such as protein kinases or protein phosphatases. Therefore, compounds that selectively bind SH2 domains can be potentially used to modulate the activity of such SH2 domain-containing enzymes. This chapter describes how to measure the regulation of protein tyrosine phosphatase activity through allosteric binding of peptides to SH2 domains, and uses human recombinant protein tyrosine phosphatase SHP2 (Src homology-2 domain-containing protein tyrosine phosphatase 2) purified from bacteria as a case example. The phosphatase activity against the artificial substrate DiFMUP (6, 8-Difluoro-4-Methylumbelliferyl Phosphate) is measured over time in the presence of a peptide that selectively binds and activates SHP2 at different concentrations to determine the half maximal effective concentration (EC50).
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Affiliation(s)
- Pablo Rios
- Faculty of Biology, Institute of Biology III, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Azin Kiani
- Faculty of Biology, Institute of Biology III, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Faculty of Chemistry and Pharmacy, University of Freiburg, Freiburg, Germany
| | - Maja Köhn
- Faculty of Biology, Institute of Biology III, University of Freiburg, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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13
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Jama M, Ahmed M, Jutla A, Wiethan C, Kumar J, Moon TC, West F, Overduin M, Barakat KH. Discovery of allosteric SHP2 inhibitors through ensemble-based consensus molecular docking, endpoint and absolute binding free energy calculations. Comput Biol Med 2023; 152:106442. [PMID: 36566625 DOI: 10.1016/j.compbiomed.2022.106442] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/05/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
SHP2 (Src homology-2 domain-containing protein tyrosine phosphatase-2) is a cytoplasmic protein -tyrosine phosphatase encoded by the gene PTPN11. It plays a crucial role in regulating cell growth and differentiation. Specifically, SHP2 is an oncoprotein associated with developmental pathologies and several different cancer types, including gastric, leukemia and breast cancer and is of great therapeutic interest. Given these roles, current research efforts have focused on developing SHP2 inhibitors. Allosteric SHP2 inhibitors have been shown to be more selective and pharmacologically appealing compared to competitive catalytic inhibitors targeting SHP2. Nevertheless, there remains a need for novel allosteric inhibitor scaffolds targeting SHP2 to develop compounds with improved selectivity, cell permeability, and bioavailability. Towards this goal, this study applied various computational tools to screen over 6 million compounds against the allosteric site within SHP2. The top-ranked hits from our in-silico screening were validated using protein thermal shift and biolayer interferometry assays, revealing three potent compounds. Kinetic binding assays were employed to measure the binding affinities of the top-ranked compounds and demonstrated that they all bind to SHP2 with a nanomolar affinity. Hence the compounds and the computational workflow described herein provide an effective approach for identifying and designing a generation of improved allosteric inhibitors of SHP2.
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Affiliation(s)
- Maryam Jama
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Canada
| | - Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Canada
| | - Anna Jutla
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Canada
| | | | - Jitendra Kumar
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Canada
| | - Tae Chul Moon
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Canada
| | - Frederick West
- Department of Chemistry, University of Alberta, Canada; Department of Oncology and Cancer Research Institute of Northern Alberta, University of Alberta, Canada
| | - Michael Overduin
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Canada
| | - Khaled H Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Canada; Li Ka Shing Institute of Virology, University of Alberta, Canada.
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14
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Sorokin AV, Kanikarla Marie P, Bitner L, Syed M, Woods M, Manyam G, Kwong LN, Johnson B, Morris VK, Jones P, Menter DG, Lee MS, Kopetz S. Targeting RAS Mutant Colorectal Cancer with Dual Inhibition of MEK and CDK4/6. Cancer Res 2022; 82:3335-3344. [PMID: 35913398 PMCID: PMC9478530 DOI: 10.1158/0008-5472.can-22-0198] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/20/2022] [Accepted: 07/26/2022] [Indexed: 01/07/2023]
Abstract
KRAS and NRAS mutations occur in 45% of colorectal cancers, with combined MAPK pathway and CDK4/6 inhibition identified as a potential therapeutic strategy. In the current study, this combinatorial treatment approach was evaluated in a co-clinical trial in patient-derived xenografts (PDX), and safety was established in a clinical trial of binimetinib and palbociclib in patients with metastatic colorectal cancer with RAS mutations. Across 18 PDX models undergoing dual inhibition of MEK and CDK4/6, 60% of tumors regressed, meeting the co-clinical trial primary endpoint. Prolonged duration of response occurred predominantly in TP53 wild-type models. Clinical evaluation of binimetinib and palbociclib in a safety lead-in confirmed safety and provided preliminary evidence of activity. Prolonged treatment in PDX models resulted in feedback activation of receptor tyrosine kinases and acquired resistance, which was reversed with a SHP2 inhibitor. These results highlight the clinical potential of this combination in colorectal cancer, along with the utility of PDX-based co-clinical trial platforms for drug development. SIGNIFICANCE This co-clinical trial of combined MEK-CDK4/6 inhibition in RAS mutant colorectal cancer demonstrates therapeutic efficacy in patient-derived xenografts and safety in patients, identifies biomarkers of response, and uncovers targetable mechanisms of resistance.
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Affiliation(s)
- Alexey V. Sorokin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Preeti Kanikarla Marie
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lea Bitner
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Muddassir Syed
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Melanie Woods
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ganiraju Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lawrence N. Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Benny Johnson
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Van K. Morris
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Philip Jones
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David G. Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael S. Lee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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15
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Asmamaw MD, Shi XJ, Zhang LR, Liu HM. A comprehensive review of SHP2 and its role in cancer. Cell Oncol 2022; 45:729-753. [PMID: 36066752 DOI: 10.1007/s13402-022-00698-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2022] [Indexed: 12/26/2022] Open
Abstract
Src homology 2-containing protein tyrosine phosphatase 2 (SHP2) is a non-receptor protein tyrosine phosphatase ubiquitously expressed mainly in the cytoplasm of several tissues. SHP2 modulates diverse cell signaling events that control metabolism, cell growth, differentiation, cell migration, transcription and oncogenic transformation. It interacts with diverse molecules in the cell, and regulates key signaling events including RAS/ERK, PI3K/AKT, JAK/STAT and PD-1 pathways downstream of several receptor tyrosine kinases (RTKs) upon stimulation by growth factors and cytokines. SHP2 acts as both a phosphatase and a scaffold, and plays prominently oncogenic functions but can be tumor suppressor in a context-dependent manner. It typically acts as a positive regulator of RTKs signaling with some inhibitory functions reported as well. SHP2 expression and activity is regulated by such factors as allosteric autoinhibition, microRNAs, ubiquitination and SUMOylation. Dysregulation of SHP2 expression or activity causes many developmental diseases, and hematological and solid tumors. Moreover, upregulated SHP2 expression or activity also decreases sensitivity of cancer cells to anticancer drugs. SHP2 is now considered as a compelling anticancer drug target and several classes of SHP2 inhibitors with different mode of action are developed with some already in clinical trial phases. Moreover, novel SHP2 substrates and functions are rapidly growing both in cell and cancer. In view of this, we comprehensively and thoroughly reviewed literatures about SHP2 regulatory mechanisms, substrates and binding partners, biological functions, roles in human cancers, and different classes of small molecule inhibitors target this oncoprotein in cancer.
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Affiliation(s)
- Moges Dessale Asmamaw
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan Province, 450001, People's Republic of China
| | - Xiao-Jing Shi
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450052, People's Republic of China
| | - Li-Rong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan Province, 450001, People's Republic of China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan Province, China. .,Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou, Henan Province, 450001, People's Republic of China.
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16
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Dai J, Zhang Y, Gao Y, Bai X, Liu F, Li S, Yu Y, Hu W, Shi T, Shi D, Li X. Toward a Treatment of Cancer: Design and In Vitro/In Vivo Evaluation of Uncharged Pyrazoline Derivatives as a Series of Novel SHP2 Inhibitors. Int J Mol Sci 2022; 23:ijms23073497. [PMID: 35408869 PMCID: PMC8998978 DOI: 10.3390/ijms23073497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/10/2022] Open
Abstract
Src homology 2 domain-containing protein tyrosine phosphatase 2 (SHP2) is a non-receptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene, which is involved in the RAS/MAPK cell signaling transduction process. SHP2 has been shown to contribute to the progression of various cancers and is emerging as an important target for anti-tumor drug research. However, past efforts to develop SHP2 inhibitors into drugs have been unsuccessful owing to the positively charged nature of the active site pocket tending to bind negatively charged groups that are usually non-drug-like. Here, a series of uncharged pyrazoline derivatives were designed and developed as new SHP2 inhibitors using a structure-based strategy. Compound 4o, which exhibited the strongest SHP2 inhibitory activity, bound directly to the catalytic domain of SHP2 in a competitive manner through multiple hydrogen bonds. Compound 4o affected the RAS/MAPK signaling pathway by inhibiting SHP2, and subsequently induced apoptosis and growth inhibition of HCT116 cells in vitro and in vivo. Notably, the oral administration of compound 4o in large doses showed no obvious toxicity. In summary, our findings provide a basis for the further development of compound 4o as a safe, effective and anti-tumor SHP2 inhibitor.
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Affiliation(s)
- Jiajia Dai
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (J.D.); (Y.Z.); (Y.G.); (X.B.); (F.L.); (S.L.); (Y.Y.); (W.H.)
| | - Yiting Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (J.D.); (Y.Z.); (Y.G.); (X.B.); (F.L.); (S.L.); (Y.Y.); (W.H.)
| | - Yanan Gao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (J.D.); (Y.Z.); (Y.G.); (X.B.); (F.L.); (S.L.); (Y.Y.); (W.H.)
| | - Xiaoyi Bai
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (J.D.); (Y.Z.); (Y.G.); (X.B.); (F.L.); (S.L.); (Y.Y.); (W.H.)
| | - Fang Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (J.D.); (Y.Z.); (Y.G.); (X.B.); (F.L.); (S.L.); (Y.Y.); (W.H.)
| | - Shuo Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (J.D.); (Y.Z.); (Y.G.); (X.B.); (F.L.); (S.L.); (Y.Y.); (W.H.)
| | - Yanyan Yu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (J.D.); (Y.Z.); (Y.G.); (X.B.); (F.L.); (S.L.); (Y.Y.); (W.H.)
| | - Wenpeng Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (J.D.); (Y.Z.); (Y.G.); (X.B.); (F.L.); (S.L.); (Y.Y.); (W.H.)
| | - Ting Shi
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China;
| | - Dayong Shi
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (J.D.); (Y.Z.); (Y.G.); (X.B.); (F.L.); (S.L.); (Y.Y.); (W.H.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Correspondence: (D.S.); (X.L.)
| | - Xiangqian Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266200, China; (J.D.); (Y.Z.); (Y.G.); (X.B.); (F.L.); (S.L.); (Y.Y.); (W.H.)
- Correspondence: (D.S.); (X.L.)
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17
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Hexachlorophene, a selective SHP2 inhibitor, suppresses proliferation and metastasis of KRAS-mutant NSCLC cells by inhibiting RAS/MEK/ERK and PI3K/AKT signaling pathways. Toxicol Appl Pharmacol 2022; 441:115988. [DOI: 10.1016/j.taap.2022.115988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 12/25/2022]
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Liu M, Gao S, Elhassan RM, Hou X, Fang H. Strategies to overcome drug resistance using SHP2 inhibitors. Acta Pharm Sin B 2021; 11:3908-3924. [PMID: 35024315 PMCID: PMC8727779 DOI: 10.1016/j.apsb.2021.03.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/17/2022] Open
Abstract
Encoded by PTPN11, the SHP2 (Src homology-2 domain-containing protein tyrosine phosphatase-2) is widely recognized as a carcinogenic phosphatase. As a promising anti-cancer drug target, SHP2 regulates many signaling pathways such as RAS-RAF-ERK, PI3K-AKT and JAK-STAT. Meanwhile, SHP2 plays a significant role in regulating immune cell function in the tumor microenvironment. Heretofore, five SHP2 allosteric inhibitors have been recruited in clinical studies for the treatment of cancer. Most recently, studies have proved the therapeutic potential of SHP2 inhibitor in overcoming drug resistance of kinase inhibitors and programmed cell death-1 (PD-1) blockade. Herein, we review the structure, function and small molecular inhibitors of SHP2, and highlight recent progress in overcoming drug resistance using SHP2 inhibitor. We hope this review would facilitate the future clinical development of SHP2 inhibitors.
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Affiliation(s)
| | | | | | - Xuben Hou
- Corresponding author. Tel./fax: +86 531 88381168.
| | - Hao Fang
- Corresponding author. Tel./fax: +86 531 88381168.
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19
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A New Paradigm for KIM-PTP Drug Discovery: Identification of Allosteric Sites with Potential for Selective Inhibition Using Virtual Screening and LEI Analysis. Int J Mol Sci 2021; 22:ijms222212206. [PMID: 34830087 PMCID: PMC8624330 DOI: 10.3390/ijms222212206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 02/04/2023] Open
Abstract
The kinase interaction motif protein tyrosine phosphatases (KIM-PTPs), HePTP, PTPSL and STEP, are involved in the negative regulation of mitogen-activated protein kinase (MAPK) signalling pathways and are important therapeutic targets for a number of diseases. We have used VSpipe, a virtual screening pipeline, to identify a ligand cluster distribution that is unique to this subfamily of PTPs. Several clusters map onto KIM-PTP specific sequence motifs in contrast to the cluster distribution obtained for PTP1B, a classic PTP that mapped to general PTP motifs. Importantly, the ligand clusters coincide with previously reported functional and substrate binding sites in KIM-PTPs. Assessment of the KIM-PTP specific clusters, using ligand efficiency index (LEI) plots generated by the VSpipe, ascertained that the binders in these clusters reside in a more drug-like chemical-biological space than those at the active site. LEI analysis showed differences between clusters across all KIM-PTPs, highlighting a distinct and specific profile for each phosphatase. The most druggable cluster sites are unexplored allosteric functional sites unique to each target. Exploiting these sites may facilitate the delivery of inhibitors with improved drug-like properties, with selectivity amongst the KIM-PTPs and over other classical PTPs.
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Nian Q, Zeng J, He L, Chen Y, Zhang Z, Rodrigues-Lima F, Zhao L, Feng X, Shi J. A small molecule inhibitor targeting SHP2 mutations for the lung carcinoma. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation. Proc Natl Acad Sci U S A 2021; 118:2025107118. [PMID: 33888588 DOI: 10.1073/pnas.2025107118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Src-homology-2 domain-containing phosphatase SHP2 is a critical regulator of signal transduction, being implicated in cell growth and differentiation. Activating mutations cause developmental disorders and act as oncogenic drivers in hematologic cancers. SHP2 is activated by phosphopeptide binding to the N-SH2 domain, triggering the release of N-SH2 from the catalytic PTP domain. Based on early crystallographic data, it has been widely accepted that opening of the binding cleft of N-SH2 serves as the key "allosteric switch" driving SHP2 activation. To test the putative coupling between binding cleft opening and SHP2 activation as assumed by the allosteric switch model, we critically reviewed structural data of SHP2, and we used extensive molecular dynamics (MD) simulation and free energy calculations of isolated N-SH2 in solution, SHP2 in solution, and SHP2 in a crystal environment. Our results demonstrate that the binding cleft in N-SH2 is constitutively flexible and open in solution and that a closed cleft found in certain structures is a consequence of crystal contacts. The degree of opening of the binding cleft has only a negligible effect on the free energy of SHP2 activation. Instead, SHP2 activation is greatly favored by the opening of the central β-sheet of N-SH2. We conclude that opening of the N-SH2 binding cleft is not the key allosteric switch triggering SHP2 activation.
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22
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Yang X, Wang Z, Pei Y, Song N, Xu L, Feng B, Wang H, Luo X, Hu X, Qiu X, Feng H, Yang Y, Zhou Y, Li J, Zhou B. Discovery of thalidomide-based PROTAC small molecules as the highly efficient SHP2 degraders. Eur J Med Chem 2021; 218:113341. [PMID: 33780898 DOI: 10.1016/j.ejmech.2021.113341] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/08/2021] [Accepted: 02/25/2021] [Indexed: 01/18/2023]
Abstract
SHP2, a non-receptor tyrosine phosphatase, plays a pivotal role in numerous oncogenic cell-signaling cascades like RAS-ERK, PI3K-AKT and JAK-STAT. On the other hand, proteolysis targeting chimera (PROTAC) has emerged as a promising strategy for the degradation of disease-related protein of interest (POI). SHP2 degradation via the PROTAC strategy will provide an alternative startegy for SHP2-mediated cancer therapy. Herein we described the design, synthesis and evaluation of a series of thalidomide-based heterobifunctional molecules and identified 11(ZB-S-29) as the highly efficient SHP2 degrader with a DC50 of 6.02 nM. Further mechanism investigation illustrated that 11 came into function through targeted SHP2 protein degradation.
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Affiliation(s)
- Xiangbo Yang
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Zhijia Wang
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Yuan Pei
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Ning Song
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China; ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Lei Xu
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Bo Feng
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China
| | - Hanlin Wang
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Xiaomin Luo
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210046, China
| | - Xiaobei Hu
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiaohui Qiu
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Huijin Feng
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yaxi Yang
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Yubo Zhou
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.
| | - Jia Li
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China; ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China; School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210046, China.
| | - Bing Zhou
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
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23
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Song Z, Wang M, Ge Y, Chen XP, Xu Z, Sun Y, Xiong XF. Tyrosine phosphatase SHP2 inhibitors in tumor-targeted therapies. Acta Pharm Sin B 2021; 11:13-29. [PMID: 33532178 PMCID: PMC7838030 DOI: 10.1016/j.apsb.2020.07.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 12/22/2022] Open
Abstract
Src homology containing protein tyrosine phosphatase 2 (SHP2) represents a noteworthy target for various diseases, serving as a well-known oncogenic phosphatase in cancers. As a result of the low cell permeability and poor bioavailability, the traditional inhibitors targeting the protein tyrosine phosphate catalytic sites are generally suffered from unsatisfactory applied efficacy. Recently, a particularly large number of allosteric inhibitors with striking inhibitory potency on SHP2 have been identified. In particular, few clinical trials conducted have made significant progress on solid tumors by using SHP2 allosteric inhibitors. This review summarizes the development and structure–activity relationship studies of the small-molecule SHP2 inhibitors for tumor therapies, with the purpose of assisting the future development of SHP2 inhibitors with improved selectivity, higher oral bioavailability and better physicochemical properties.
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Key Words
- ALK, anaplastic lymphoma kinase
- AML, acute myeloid leukemia
- Allosteric inhibitor
- B-ALL, B-cell acute lymphoblastic leukemia
- BTLA, B and T lymphocyte attenuator
- CADD, computer aided drug design
- CSF-1, colony stimulating factor-1
- CTLA-4, cytotoxic T lymphocyte-associated antigen-4
- EGFR, epidermal growth factor receptor
- ERK1/2, extracelluar signal-regulated kinase 1/2
- FLT3, Fms-like tyrosine kinase-3
- GAB2, Grb2-associated binding protein-2
- GRB2, growth factor receptor-bound protein 2
- HER2, human epidermal growth factor receptor-2
- HGF/SF, hepatocyte growth factor/scatter factor
- JAK, Janus kinase
- KRAS, v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
- MAPK, mitogen-activated protein kinase
- NLRP3, NLR family, pyrin domain containing protein 3
- PD-1/PDL-1, programmed cell death protein-1/programmed death ligand-1
- PDAC, pancreatic ductal adenocarcinoma
- PDX, patient-derived xenograft
- PI3K, phosphatidylinositol 3 kinase
- PTK, protein tyrosine kinase
- PTP, protein tyrosine phosphatase
- Phosphatase
- RAS, rat sarcoma protein
- RTKs, receptor tyrosine kinase inhibitors
- SAR, structure–activity relationship
- SBDD, structure-based drug design
- SCC, squamous cell carcinoma
- SCNA, somatic copy number change
- SHP2
- SHP2, Src homology containing protein tyrosine phosphatase 2
- STAT, signal transducers and activators of transcription
- Selectivity
- TIGIT, T-cell immunoglobulin and ITIM domain protein
- TKIs, tyrosine kinase inhibitors
- Tumor therapy
- hERG, human ether-a-go-go-related gene
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Affiliation(s)
- Zhendong Song
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Meijing Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yang Ge
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xue-Ping Chen
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ziyang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiao-Feng Xiong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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24
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Qian P, Mu XT, Su B, Gao L, Zhang DF. Identification of the anti-breast cancer targets of triterpenoids in Liquidambaris Fructus and the hints for its traditional applications. BMC Complement Med Ther 2020; 20:369. [PMID: 33246450 PMCID: PMC7694930 DOI: 10.1186/s12906-020-03143-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/31/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Liquidambaris Fructus is the infructescences of Liquidambar formosana Hance and it has been used to treat some breast disease in Traditional Chinese Medicine. In the previous study we found the anti-breast cancer effect of triterpenoid in Liquidambaris Fructus. This study is a further investigation of the triterpenoids in Liquidambaris Fructus and aims to identify their anti-breast cancer targets, meanwhile, to estimate the rationality of the traditional applications of Liquidambaris Fructus. METHODS Triterpenoids in Liquidambaris Fructus were isolated and their structures were identified by NMR spectrums. Potential targets of these triterpenoids were predicted using a reverse pharmacophore mapping strategy. Associations between these targets and the therapeutic targets of breast cancer were analyzed by constructing protein-protein interaction network, and targets played important roles in the network were identified using Molecular Complex Detection method. Binding affinity between the targets and triterpenoids was studied using molecular docking method. Gene ontology enrichment analysis was conducted to reveal the biological process and signaling pathways that the identified targets were involved in. RESULTS Thirteen triterpenoids were identified and 6 of them were the first time isolated from Liquidambaris Fructus. Predicted ADME properties revealed a good druggability of these triterpenoids. We identified 18 protein targets which were closely related to breast cancer progression, especially triple-negative, basal-like or advanced stage breast cancers. The triterpenoids could bind with these targets as their inhibitors: hydrophobic skeleton is a favorable factor for them to stabilize at binding site and polar C17- or C3- substituent was necessary for binding. GO enrichment analysis indicated that inhibition of protein tyrosine kinases autophosphorylation might be the primary mechanism for the anti-breast cancer effect of the triterpenoids, and ErbB4 and EGFR were the most relevant targets. CONCLUSIONS The study revealed that triterpenoids from Liquidambaris Fructus might exert anti-breast cancer effect by directly inhibit multiple protein targets and signaling pathways, especially ErbB4 and EGFR and related pathways. This study also brings up another hint that the traditional applications of Liquidambaris Fructus on hypogalactia should be reassessed systematically because it might suppress rather than promote lactation by inhibiting the activity of ErbB4.
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Affiliation(s)
- Ping Qian
- Department of Pharmacognosy, School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Xiao-Ting Mu
- Department of Pharmacognosy, School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Bing Su
- Department of Pharmacognosy, School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Lu Gao
- Department of Pharmacognosy, School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Dong-Fang Zhang
- Department of Pharmacognosy, School of Pharmacy, China Medical University, Shenyang, 110122, China.
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25
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Tripathi RKP, Ayyannan SR. Emerging chemical scaffolds with potential SHP2 phosphatase inhibitory capabilities - A comprehensive review. Chem Biol Drug Des 2020; 97:721-773. [PMID: 33191603 DOI: 10.1111/cbdd.13807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022]
Abstract
The drug discovery panorama is cluttered with promising therapeutic targets that have been deserted because of inadequate authentication and screening failures. Molecular targets formerly tagged as "undruggable" are nowadays being more cautiously cross-examined, and whilst they stay intriguing, numerous targets are emerging more accessible. Protein tyrosine phosphatases (PTPs) excellently exemplifies a class of molecular targets that have transpired as druggable, with several small molecules and antibodies recently turned available for further development. In this respect, SHP2, a PTP, has emerged as one of the potential targets in the current pharmacological research, particularly for cancer, due to its critical role in various signalling pathways. Recently, few molecules with excellent potency have entered clinical trials, but none could reach the clinic. Consequently, search for novel, non-toxic, and specific SHP2 inhibitors are on purview. In this review, general aspects of SHP2 including its structure and mechanistic role in carcinogenesis have been presented. It also sheds light on the development of novel molecular architectures belonging to diverse chemical classes that have been proposed as SHP2-specific inhibitors along with their structure-activity relationships (SARs), stemming from chemical, mechanism-based and computer-aided studies reported since January 2015 to July 2020 (excluding patents), focusing on their potency and selectivity. The encyclopedic facts and discussions presented herein will hopefully facilitate researchers to design new ligands with better efficacy and selectivity against SHP2.
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Affiliation(s)
- Rati Kailash Prasad Tripathi
- Department of Pharmaceutical Science, Sushruta School of Medical and Paramedical Sciences, Assam University (A Central University), Silchar, Assam, India.,Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Senthil Raja Ayyannan
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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26
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Anselmi M, Hub JS. An allosteric interaction controls the activation mechanism of SHP2 tyrosine phosphatase. Sci Rep 2020; 10:18530. [PMID: 33116231 PMCID: PMC7595171 DOI: 10.1038/s41598-020-75409-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/13/2020] [Indexed: 12/20/2022] Open
Abstract
SHP2 is a protein tyrosine phosphatase (PTP) involved in multiple signaling pathways. Mutations of SHP2 can result in Noonan syndrome or pediatric malignancies. Inhibition of wild-type SHP2 represents a novel strategy against several cancers. SHP2 is activated by binding of a phosphopeptide to the N-SH2 domain of SHP2, thereby favoring dissociation of the N-SH2 domain and exposing the active site on the PTP domain. The conformational transitions controlling ligand affinity and PTP dissociation remain poorly understood. Using molecular simulations, we revealed an allosteric interaction restraining the N-SH2 domain into a SHP2-activating and a stabilizing state. Only ligands selecting for the activating N-SH2 conformation, depending on ligand sequence and binding mode, are effective activators. We validate the model of SHP2 activation by rationalizing modified basal activity and responsiveness to ligand stimulation of several N-SH2 variants. This study provides mechanistic insight into SHP2 activation and may open routes for SHP2 regulation.
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Affiliation(s)
- Massimiliano Anselmi
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, 37077, Göttingen, Germany. .,Theoretical Physics and Center for Biophysics, Saarland University, Campus E2.6, 66123, Saarbrücken, Germany.
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2.6, 66123, Saarbrücken, Germany
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27
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LaMarche MJ, Acker M, Argintaru A, Bauer D, Boisclair J, Chan H, Chen CHT, Chen YN, Chen Z, Deng Z, Dore M, Dunstan D, Fan J, Fekkes P, Firestone B, Fodor M, Garcia-Fortanet J, Fortin PD, Fridrich C, Giraldes J, Glick M, Grunenfelder D, Hao HX, Hentemann M, Ho S, Jouk A, Kang ZB, Karki R, Kato M, Keen N, Koenig R, LaBonte LR, Larrow J, Liu G, Liu S, Majumdar D, Mathieu S, Meyer MJ, Mohseni M, Ntaganda R, Palermo M, Perez L, Pu M, Ramsey T, Reilly J, Sarver P, Sellers WR, Sendzik M, Shultz MD, Slisz J, Slocum K, Smith T, Spence S, Stams T, Straub C, Tamez V, Toure BB, Towler C, Wang P, Wang H, Williams SL, Yang F, Yu B, Zhang JH, Zhu S. Identification of TNO155, an Allosteric SHP2 Inhibitor for the Treatment of Cancer. J Med Chem 2020; 63:13578-13594. [PMID: 32910655 DOI: 10.1021/acs.jmedchem.0c01170] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SHP2 is a nonreceptor protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also plays an important role in the programed cell death pathway (PD-1/PD-L1). As an oncoprotein as well as a potential immunomodulator, controlling SHP2 activity is of high therapeutic interest. As part of our comprehensive program targeting SHP2, we identified multiple allosteric binding modes of inhibition and optimized numerous chemical scaffolds in parallel. In this drug annotation report, we detail the identification and optimization of the pyrazine class of allosteric SHP2 inhibitors. Structure and property based drug design enabled the identification of protein-ligand interactions, potent cellular inhibition, control of physicochemical, pharmaceutical and selectivity properties, and potent in vivo antitumor activity. These studies culminated in the discovery of TNO155, (3S,4S)-8-(6-amino-5-((2-amino-3-chloropyridin-4-yl)thio)pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine (1), a highly potent, selective, orally efficacious, and first-in-class SHP2 inhibitor currently in clinical trials for cancer.
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28
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Phosphatase-independent functions of SHP2 and its regulation by small molecule compounds. J Pharmacol Sci 2020; 144:139-146. [PMID: 32921395 DOI: 10.1016/j.jphs.2020.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
SHP2 is a non-receptor protein tyrosine phosphatase encoded by the PTPN11 gene in human. Clinically, SHP2 has been identified as a causal factor of several diseases, such as Noonan syndrome, LEOPARD syndrome as well as myeloid malignancies. Interestingly, both loss-of-function and gain-of-function mutations occur in the PTPN11 gene. Analyses by biochemical and cell biological means as well as probing with small molecule compounds have demonstrated that SHP2 has both phosphatase-dependent and independent functions. In comparison with its phosphatase activity, the non-phosphatase-like function of SHP2 has not been well introduced or summarized. This review mainly focuses on the phosphatase-independent functions and its regulation by small molecule compounds as well as their use for disease therapy.
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29
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Tang K, Jia YN, Yu B, Liu HM. Medicinal chemistry strategies for the development of protein tyrosine phosphatase SHP2 inhibitors and PROTAC degraders. Eur J Med Chem 2020; 204:112657. [PMID: 32738411 DOI: 10.1016/j.ejmech.2020.112657] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 12/20/2022]
Abstract
As a non-receptor protein tyrosine phosphatase encoded by the PTPN11 gene, the Src homology 2 domain-containing protein tyrosine phosphatase (SHP2) is involved in mitogen-activated protein kinase (MAPK) signaling pathway and contributes to immune surveillance via programmed cell death pathway (PD-1/PD-L1). To date, numerous SHP2 inhibitors have been developed, some of them have advanced into clinical trials. Moreover, the first PROTAC degrader SHP2-D26 has been proved to effectively induce degradation of SHP2, which may open a new avenue for targeted SHP2 therapies. In this review, we systematically summarized the development of SHP2 inhibitors with a particular focus on the structure-activity relationships (SAR) studies, crystal structures or binding models, and their modes of action.
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Affiliation(s)
- Kai Tang
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Military of Education, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yao-Nan Jia
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Military of Education, Zhengzhou University, Zhengzhou, 450001, China.
| | - Bin Yu
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Military of Education, Zhengzhou University, Zhengzhou, 450001, China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Military of Education, Zhengzhou University, Zhengzhou, 450001, China.
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30
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Zhu L, Roberts R, Huang R, Zhao J, Xia M, Delavan B, Mikailov M, Tong W, Liu Z. Drug Repositioning for Noonan and LEOPARD Syndromes by Integrating Transcriptomics With a Structure-Based Approach. Front Pharmacol 2020; 11:927. [PMID: 32676024 PMCID: PMC7333460 DOI: 10.3389/fphar.2020.00927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 06/08/2020] [Indexed: 01/24/2023] Open
Abstract
Noonan and LEOPARD syndromes (NS and LS) belong to a group of related disorders called RASopathies characterized by abnormalities of multiple organs and systems including hypertrophic cardiomyopathy and dysmorphic facial features. There are no approved drugs for these two rare diseases, but it is known that a missense mutation in PTPN11 genes is associated with approximately 50% and 70% of NS and LS cases, respectively. In this study, we implemented a hybrid computational drug repositioning framework by integrating transcriptomic and structure-based approaches to explore potential treatment options for NS and LS. Specifically, disease signatures were derived from the transcriptomic profiles of human induced pluripotent stem cells (iPSCs) from NS and LS patients and reverse correlated to drug transcriptomic signatures from CMap and L1000 projects on the basis that if disease and drug transcriptomic signatures are reversely correlated, the drug has the potential to treat that disease. The compounds that were ranked top based on their transcriptomic profiles were docked to mutated and wild-type 3D structures of PTPN11 by an adjusted Induced Fit Docking (IFD) protocol. In addition, we prioritized repositioned candidates for NS and LS by a consensus ranking strategy. Network analysis and phenotypic anchoring of the transcriptomic data could discriminate the two diseases at the molecular level. Furthermore, the adjusted IFD protocol was able to recapitulate the binding specificity of potential drug candidates to mutated 3D structures, revealing the relevant amino acids. Importantly, a list of potential drug candidates for repositioning was identified including 61 for NS and 43 for LS and was further verified from literature reports and on-going clinical trials. Altogether, this hybrid computational drug repositioning approach has highlighted a number of drug candidates for NS and LS and could be applied to identifying drug candidates for other diseases as well.
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Affiliation(s)
- Liyuan Zhu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Ruth Roberts
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States.,Department of Drug Safety, ApconiX, Alderley Edge, United Kingdom.,Department of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Jinghua Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Brian Delavan
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States.,Joint Bioinformatics Graduate Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Mike Mikailov
- Office of Science and Engineering Labs, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Zhichao Liu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
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31
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Anselmi M, Calligari P, Hub JS, Tartaglia M, Bocchinfuso G, Stella L. Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase. J Chem Inf Model 2020; 60:3157-3171. [PMID: 32395997 PMCID: PMC8007070 DOI: 10.1021/acs.jcim.0c00307] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Indexed: 11/28/2022]
Abstract
SH2 domain-containing tyrosine phosphatase 2 (SHP2), encoded by PTPN11, plays a fundamental role in the modulation of several signaling pathways. Germline and somatic mutations in PTPN11 are associated with different rare diseases and hematologic malignancies, and recent studies have individuated SHP2 as a central node in oncogenesis and cancer drug resistance. The SHP2 structure includes two Src homology 2 domains (N-SH2 and C-SH2) followed by a catalytic protein tyrosine phosphatase (PTP) domain. Under basal conditions, the N-SH2 domain blocks the active site, inhibiting phosphatase activity. Association of the N-SH2 domain with binding partners containing short amino acid motifs comprising a phosphotyrosine residue (pY) leads to N-SH2/PTP dissociation and SHP2 activation. Considering the relevance of SHP2 in signaling and disease and the central role of the N-SH2 domain in its allosteric regulation mechanism, we performed microsecond-long molecular dynamics (MD) simulations of the N-SH2 domain complexed to 12 different peptides to define the structural and dynamical features determining the binding affinity and specificity of the domain. Phosphopeptide residues at position -2 to +5, with respect to pY, have significant interactions with the SH2 domain. In addition to the strong interaction of the pY residue with its conserved binding pocket, the complex is stabilized hydrophobically by insertion of residues +1, +3, and +5 in an apolar groove of the domain and interaction of residue -2 with both the pY and a protein surface residue. Additional interactions are provided by hydrogen bonds formed by the backbone of residues -1, +1, +2, and +4. Finally, negatively charged residues at positions +2 and +4 are involved in electrostatic interactions with two lysines (Lys89 and Lys91) specific for the SHP2 N-SH2 domain. Interestingly, the MD simulations illustrated a previously undescribed conformational flexibility of the domain, involving the core β sheet and the loop that closes the pY binding pocket.
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Affiliation(s)
- Massimiliano Anselmi
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
| | - Paolo Calligari
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
| | - Jochen S. Hub
- Theoretical
Physics and Center for Biophysics, Saarland
University, Campus E2 6, 66123 Saarbrücken, Germany
| | - Marco Tartaglia
- Genetics
and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Gianfranco Bocchinfuso
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
| | - Lorenzo Stella
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
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Satheeshkumar R, Zhu R, Feng B, Huang C, Gao Y, Gao LX, Shen C, Hou TJ, Xu L, Li J, Zhu YL, Zhou YB, Wang WL. Synthesis and biological evaluation of heterocyclic bis-aryl amides as novel Src homology 2 domain containing protein tyrosine phosphatase-2 (SHP2) inhibitors. Bioorg Med Chem Lett 2020; 30:127170. [DOI: 10.1016/j.bmcl.2020.127170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 02/03/2023]
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33
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Chen CD, Zeldich E, Khodr C, Camara K, Tung TY, Lauder EC, Mullen P, Polanco TJ, Liu YY, Zeldich D, Xia W, Van Nostrand WE, Brown LE, Porco JA, Abraham CR. Small Molecule Amyloid-β Protein Precursor Processing Modulators Lower Amyloid-β Peptide Levels via cKit Signaling. J Alzheimers Dis 2020; 67:1089-1106. [PMID: 30776010 DOI: 10.3233/jad-180923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer's disease (AD) is characterized by the accumulation of neurotoxic amyloid-β (Aβ) peptides consisting of 39-43 amino acids, proteolytically derived fragments of the amyloid-β protein precursor (AβPP), and the accumulation of the hyperphosphorylated microtubule-associated protein tau. Inhibiting Aβ production may reduce neurodegeneration and cognitive dysfunction associated with AD. We have previously used an AβPP-firefly luciferase enzyme complementation assay to conduct a high throughput screen of a compound library for inhibitors of AβPP dimerization, and identified a compound that reduces Aβ levels. In the present study, we have identified an analog, compound Y10, which also reduced Aβ. Initial kinase profiling assays identified the receptor tyrosine kinase cKit as a putative Y10 target. To elucidate the precise mechanism involved, AβPP phosphorylation was examined by IP-western blotting. We found that Y10 inhibits cKit phosphorylation and increases AβPP phosphorylation mainly on tyrosine residue Y743, according to AβPP751 numbering. A known cKit inhibitor and siRNA specific to cKit were also found to increase AβPP phosphorylation and lower Aβ levels. We also investigated a cKit downstream signaling molecule, the Shp2 phosphatase, and found that known Shp2 inhibitors and siRNA specific to Shp2 also increase AβPP phosphorylation, suggesting that the cKit signaling pathway is also involved in AβPP phosphorylation and Aβ production. We further found that inhibitors of both cKit and Shp2 enhance AβPP surface localization. Thus, regulation of AβPP phosphorylation by small molecules should be considered as a novel therapeutic intervention for AD.
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Affiliation(s)
- Ci-Di Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Ella Zeldich
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Christina Khodr
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Kaddy Camara
- Department of Chemistry, Boston University, Boston, MA, USA.,Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - Tze Yu Tung
- Department of Biology, Boston University, Boston, MA, USA
| | - Emma C Lauder
- Department of Neuroscience, Boston University, Boston, MA, USA
| | - Patrick Mullen
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Taryn J Polanco
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Yen-Yu Liu
- Department of Biology, Boston University, Boston, MA, USA
| | - Dean Zeldich
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Weiming Xia
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.,Bedford Geriatric Research Education Clinical Center, Bedford VA Medical Center, Bedford, MA, USA
| | - William E Van Nostrand
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI, USA
| | - Lauren E Brown
- Department of Chemistry, Boston University, Boston, MA, USA.,Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA.,Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - John A Porco
- Department of Chemistry, Boston University, Boston, MA, USA.,Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - Carmela R Abraham
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.,Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
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34
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Wang M, Lu J, Wang M, Yang CY, Wang S. Discovery of SHP2-D26 as a First, Potent, and Effective PROTAC Degrader of SHP2 Protein. J Med Chem 2020; 63:7510-7528. [DOI: 10.1021/acs.jmedchem.0c00471] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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35
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Köhn M. Turn and Face the Strange: A New View on Phosphatases. ACS CENTRAL SCIENCE 2020; 6:467-477. [PMID: 32341996 PMCID: PMC7181316 DOI: 10.1021/acscentsci.9b00909] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Indexed: 05/08/2023]
Abstract
Phosphorylation as a post-translational modification is critical for cellular homeostasis. Kinases and phosphatases regulate phosphorylation levels by adding or removing, respectively, a phosphate group from proteins or other biomolecules. Imbalances in phosphorylation levels are involved in a multitude of diseases. Phosphatases are often thought of as the black sheep, the strangers, of phosphorylation-mediated signal transduction, particularly when it comes to drug discovery and development. This is due to past difficulties to study them and unsuccessful attempts to target them; however, phosphatases have regained strong attention and are actively pursued now in clinical trials. By giving examples for current hot topics in phosphatase biology and for new approaches to target them, it is illustrated here how and why phosphatases made their comeback, and what is envisioned to come in the future.
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Affiliation(s)
- Maja Köhn
- Faculty
of Biology, Institute of Biology III, University
of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Signalling
Research Centres BIOSS and CIBSS, University
of Freiburg, Freiburg, Germany
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36
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Wu J, Li W, Zheng Z, Lu X, Zhang H, Ma Y, Wang R. Design, synthesis, biological evaluation, common feature pharmacophore model and molecular dynamics simulation studies of ethyl 4-(phenoxymethyl)-2-phenylthiazole-5-carboxylate as Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2) inhibitors. J Biomol Struct Dyn 2020; 39:1174-1188. [PMID: 32036779 DOI: 10.1080/07391102.2020.1726817] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SHP2 is a non-receptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene involved in cell death pathway (PD-1/PD-L1) and cell growth and differentiation pathway (MAPK). Moreover, mutations in SHP2 have been implicated in Leopard syndrome (LS), Noonan syndrome (NS), juvenile myelomonocytic leukemia (JMML) and several types of cancer and solid tumors. Thus, SHP2 inhibitors are much needed reagents for evaluation of SHP2 as a therapeutic target. A series of novel ethyl 4-(phenoxymethyl)-2-phenylthiazole-5-carboxylate derivatives were designed and synthesized, and their SHP2 inhibitory activities (IC50) were determined. Among the desired compounds, 1d shares the highest inhibitory activity (IC50 = 0.99 μM) against SHP2. Additionally, a common feature pharmacophore model was established to explain the structure activity relationship of the desired compounds. Finally, molecular dynamics simulation was carried out to explore the most likely binding mode of compound 1d with SHP2. In brief, the findings reported here may at least provide a new strategy or useful insights in discovering novel effective SHP2 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jingwei Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Weiya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Zhihui Zheng
- New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering and Research Center, Hebei Industry Microbial Metabolic Engineering &Technology Research Center, Key Laboratory for New Drug, Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Xinhua Lu
- New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering and Research Center, Hebei Industry Microbial Metabolic Engineering &Technology Research Center, Key Laboratory for New Drug, Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Huan Zhang
- Department of Pharmacy, Tianjin Medical University General Hospital, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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37
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Therapeutic potential of targeting SHP2 in human developmental disorders and cancers. Eur J Med Chem 2020; 190:112117. [PMID: 32061959 DOI: 10.1016/j.ejmech.2020.112117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 02/06/2023]
Abstract
Src homology 2 (SH2)-containing protein tyrosine phosphatase 2 (SHP2), encoded by PTPN11, regulates cell proliferation, differentiation, apoptosis and survival via releasing intramolecular autoinhibition and modulating various signaling pathways, such as mitogen-activated protein kinase (MAPK) pathway. Mutations and aberrant expression of SHP2 are implicated in human developmental disorders, leukemias and several solid tumors. As an oncoprotein in some cancers, SHP2 represents a rational target for inhibitors to interfere. Nevertheless, its tumor suppressive effect has also been uncovered, indicating the context-specificity. Even so, two types of SHP2 inhibitors including targeting catalytic pocket and allosteric sites have been developed associated with resolved cocrystal complexes. Herein, we describe its structure, biological function, deregulation in human diseases and summarize recent advance in development of SHP2 inhibitors, trying to give an insight into the therapeutic potential in future.
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38
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Marasco M, Berteotti A, Weyershaeuser J, Thorausch N, Sikorska J, Krausze J, Brandt HJ, Kirkpatrick J, Rios P, Schamel WW, Köhn M, Carlomagno T. Molecular mechanism of SHP2 activation by PD-1 stimulation. SCIENCE ADVANCES 2020; 6:eaay4458. [PMID: 32064351 PMCID: PMC6994217 DOI: 10.1126/sciadv.aay4458] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/22/2019] [Indexed: 05/02/2023]
Abstract
In cancer, the programmed death-1 (PD-1) pathway suppresses T cell stimulation and mediates immune escape. Upon stimulation, PD-1 becomes phosphorylated at its immune receptor tyrosine-based inhibitory motif (ITIM) and immune receptor tyrosine-based switch motif (ITSM), which then bind the Src homology 2 (SH2) domains of SH2-containing phosphatase 2 (SHP2), initiating T cell inactivation. The SHP2-PD-1 complex structure and the exact functions of the two SH2 domains and phosphorylated motifs remain unknown. Here, we explain the structural basis and provide functional evidence for the mechanism of PD-1-mediated SHP2 activation. We demonstrate that full activation is obtained only upon phosphorylation of both ITIM and ITSM: ITSM binds C-SH2 with strong affinity, recruiting SHP2 to PD-1, while ITIM binds N-SH2, displacing it from the catalytic pocket and activating SHP2. This binding event requires the formation of a new inter-domain interface, offering opportunities for the development of novel immunotherapeutic approaches.
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Affiliation(s)
- M. Marasco
- Leibniz University Hannover, Institute of Organic Chemistry and Center for Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany
| | - A. Berteotti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - J. Weyershaeuser
- Faculty of Biology, Institute of Biology III, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - N. Thorausch
- Faculty of Biology, Institute of Biology III, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - J. Sikorska
- Helmholtz Centre for Infection Research, Group of Structural Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - J. Krausze
- Leibniz University Hannover, Institute of Organic Chemistry and Center for Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany
| | - H. J. Brandt
- Faculty of Biology, Institute of Biology III, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - J. Kirkpatrick
- Leibniz University Hannover, Institute of Organic Chemistry and Center for Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany
- Helmholtz Centre for Infection Research, Group of Structural Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - P. Rios
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Faculty of Biology, Institute of Biology III, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - W. W. Schamel
- Faculty of Biology, Institute of Biology III, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Center of Chronic Immunodeficiency CCI, University Clinics and Medical Faculty, Freiburg, Germany
| | - M. Köhn
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Faculty of Biology, Institute of Biology III, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Corresponding author. (T.C.); (M.K.)
| | - T. Carlomagno
- Leibniz University Hannover, Institute of Organic Chemistry and Center for Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Helmholtz Centre for Infection Research, Group of Structural Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Corresponding author. (T.C.); (M.K.)
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39
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Niogret C, Birchmeier W, Guarda G. SHP-2 in Lymphocytes' Cytokine and Inhibitory Receptor Signaling. Front Immunol 2019; 10:2468. [PMID: 31708921 PMCID: PMC6823243 DOI: 10.3389/fimmu.2019.02468] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/03/2019] [Indexed: 02/06/2023] Open
Abstract
Somewhat counterintuitively, the tyrosine phosphatase SHP-2 (SH2 domain-containing protein tyrosine phosphatase-2) is crucial for the activation of extracellular signal-regulated kinase (ERK) downstream of various growth factor receptors, thereby exerting essential developmental functions. This phosphatase also deploys proto-oncogenic functions and specific inhibitors have recently been developed. With respect to the immune system, the role of SHP-2 in the signaling of cytokines relevant for myelopoiesis and myeloid malignancies has been intensively studied. The function of this phosphatase downstream of cytokines important for lymphocytes is less understood, though multiple lines of evidence suggest its importance. In addition, SHP-2 has been proposed to mediate the suppressive effects of inhibitory receptors (IRs) that sustain a dysfunctional state in anticancer T cells. Molecules involved in IR signaling are of potential pharmaceutical interest as blockade of these inhibitory circuits leads to remarkable clinical benefit. Here, we discuss the dichotomy in the functions ascribed to SHP-2 downstream of cytokine receptors and IRs, with a focus on T and NK lymphocytes. Further, we highlight the importance of broadening our understanding of SHP-2′s relevance in lymphocytes, an essential step to inform on side effects and unanticipated benefits of its therapeutic blockade.
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Affiliation(s)
- Charlène Niogret
- Department of Biochemistry, University of Lausanne, Épalinges, Switzerland
| | - Walter Birchmeier
- Max-Delbrueck-Center for Molecular Medicine (MDC) in the Helmholtz Society, Berlin, Germany
| | - Greta Guarda
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
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40
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Wang RR, Liu WS, Zhou L, Ma Y, Wang RL. Probing the acting mode and advantages of RMC-4550 as an Src-homology 2 domain-containing protein tyrosine phosphatase (SHP2) inhibitor at molecular level through molecular docking and molecular dynamics. J Biomol Struct Dyn 2019; 38:1525-1538. [DOI: 10.1080/07391102.2019.1613266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wen-Shan Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Liang Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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41
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Bagdanoff JT, Chen Z, Acker M, Chen YN, Chan H, Dore M, Firestone B, Fodor M, Fortanet J, Hentemann M, Kato M, Koenig R, LaBonte LR, Liu S, Mohseni M, Ntaganda R, Sarver P, Smith T, Sendzik M, Stams T, Spence S, Towler C, Wang H, Wang P, Williams SL, LaMarche MJ. Optimization of Fused Bicyclic Allosteric SHP2 Inhibitors. J Med Chem 2019; 62:1781-1792. [DOI: 10.1021/acs.jmedchem.8b01725] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Movarid Mohseni
- Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | | | | | | | | | | | | | - Christopher Towler
- Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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42
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Sarver P, Acker M, Bagdanoff JT, Chen Z, Chen YN, Chan H, Firestone B, Fodor M, Fortanet J, Hao H, Hentemann M, Kato M, Koenig R, LaBonte LR, Liu G, Liu S, Liu C, McNeill E, Mohseni M, Sendzik M, Stams T, Spence S, Tamez V, Tichkule R, Towler C, Wang H, Wang P, Williams SL, Yu B, LaMarche MJ. 6-Amino-3-methylpyrimidinones as Potent, Selective, and Orally Efficacious SHP2 Inhibitors. J Med Chem 2019; 62:1793-1802. [DOI: 10.1021/acs.jmedchem.8b01726] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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43
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Marsh-Armstrong B, Fajnzylber JM, Korntner S, Plaman BA, Bishop AC. The Allosteric Site on SHP2's Protein Tyrosine Phosphatase Domain is Targetable with Druglike Small Molecules. ACS OMEGA 2018; 3:15763-15770. [PMID: 30533581 PMCID: PMC6275946 DOI: 10.1021/acsomega.8b02200] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/23/2018] [Indexed: 06/09/2023]
Abstract
Difficulties in developing active-site-directed protein tyrosine phosphatase (PTP) inhibitors have led to the perception that PTPs are "undruggable", highlighting the need for new means to target pharmaceutically important PTPs allosterically. Recently, we characterized an allosteric-inhibition site on the PTP domain of Src-homology-2-domain-containing PTP 2 (SHP2), a key anticancer drug target. The central feature of SHP2's allosteric site is a nonconserved cysteine residue (C333) that can potentially be labeled with electrophilic compounds for selective SHP2 inhibition. Here, we describe the first directed discovery effort for C333-targeted allosteric SHP2 inhibitors. By screening a previously reported library of reversible, covalent inhibitors, we identified a lead compound, which was modified to yield an irreversible inhibitor (12), that inhibits SHP2 allosterically and selectively through interaction with C333. These findings provide a novel paradigm for allosteric-inhibitor discovery on SHP2, one that may help to circumvent the challenges inherent in targeting SHP2's active site.
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44
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Farrokhzadeh A, Akher FB, Soliman MES. Probing the Dynamic Mechanism of Uncommon Allosteric Inhibitors Optimized to Enhance Drug Selectivity of SHP2 with Therapeutic Potential for Cancer Treatment. Appl Biochem Biotechnol 2018; 188:260-281. [DOI: 10.1007/s12010-018-2914-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/05/2018] [Indexed: 01/24/2023]
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45
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Tsutsumi R, Ran H, Neel BG. Off-target inhibition by active site-targeting SHP2 inhibitors. FEBS Open Bio 2018; 8:1405-1411. [PMID: 30186742 PMCID: PMC6120237 DOI: 10.1002/2211-5463.12493] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/19/2018] [Accepted: 06/05/2018] [Indexed: 01/04/2023] Open
Abstract
Due to the involvement of SHP2 (SH2 domain-containing protein-tyrosine phosphatase) in human disease, including Noonan syndrome and cancer, several inhibitors targeting SHP2 have been developed. Here, we report that the commonly used SHP2 inhibitor NSC-87877 does not exhibit robust inhibitory effects on growth factor-dependent MAPK (mitogen-activated protein kinase) pathway activation and that the recently developed active site-targeting SHP2 inhibitors IIB-08, 11a-1, and GS-493 show off-target effects on ligand-evoked activation/trans-phosphorylation of the PDGFRβ (platelet-derived growth factor receptor β). GS-493 also inhibits purified human PDGFRβ and SRC in vitro, whereas PDGFRβ inhibition by IIB-08 and 11a-1 occurs only in the cellular context. Our results argue for extreme caution in inferring specific functions for SHP2 based on studies using these inhibitors.
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Affiliation(s)
- Ryouhei Tsutsumi
- Laura and Isaac Perlmutter Cancer CenterNYU Langone HealthNew YorkNYUSA
| | - Hao Ran
- Laura and Isaac Perlmutter Cancer CenterNYU Langone HealthNew YorkNYUSA
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer CenterNYU Langone HealthNew YorkNYUSA
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46
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Vazhappilly CG, Saleh E, Ramadan W, Menon V, Al-Azawi AM, Tarazi H, Abdu-Allah H, El-Shorbagi AN, El-Awady R. Inhibition of SHP2 by new compounds induces differential effects on RAS/RAF/ERK and PI3K/AKT pathways in different cancer cell types. Invest New Drugs 2018; 37:252-261. [PMID: 29947013 DOI: 10.1007/s10637-018-0626-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
Abstract
Kinases and phosphatases are important players in growth signaling and are involved in cancer development. For development of targeted cancer therapy, attention is given to kinases rather than phosphatases inhibitors. Src homology region 2 domain-containing protein tyrosine phosphatase2 (SHP2) is overexpressed in different types of cancers. We investigated the SHP2-inhibitory effects of two new 5-aminosalicylate-4-thiazolinones in human cervical (HeLa) and breast (MCF-7 & MDA-MB-231) cancer cells. In-silico molecular docking showed preferential affinity of the two compounds towards the catalytic over the allosteric site of SHP2. An enzymatic assay confirmed the docking results whereby 0.01 μM of both compounds reduced SHP2 activity to 50%. On cellular level, the two compounds significantly reduced the expression of SHP2, KRAS, p-ERK and p-STAT3 in HeLa but not in the other two cell lines. Phosphorylation of AKT and JNK was enhanced in HeLa and MCF7. Both compounds exhibited anti-proliferative/anti-migratory effects on HeLa and MCF7 but not in MDA-MB-231 cells. These results indicate that inhibition of SHP2 and its downstream pathways by the two compounds might be a promising strategy for cancer therapy in some but not all cancer types.
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Affiliation(s)
- Cijo George Vazhappilly
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Ekram Saleh
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Wafaa Ramadan
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Varsha Menon
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Aya Mudhafar Al-Azawi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Hamadeh Tarazi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy, University of Sharjah, University City Road, 27272, Sharjah, United Arab Emirates
| | - Hajjaj Abdu-Allah
- Medicinal Chemistry Department, College of Pharmacy, Assuit University, Assuit, Egypt
| | - Abdel-Nasser El-Shorbagi
- College of Pharmacy, University of Sharjah, University City Road, 27272, Sharjah, United Arab Emirates.,Medicinal Chemistry Department, College of Pharmacy, Assuit University, Assuit, Egypt
| | - Raafat El-Awady
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates. .,College of Pharmacy, University of Sharjah, University City Road, 27272, Sharjah, United Arab Emirates.
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47
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Fodor M, Price E, Wang P, Lu H, Argintaru A, Chen Z, Glick M, Hao HX, Kato M, Koenig R, LaRochelle JR, Liu G, McNeill E, Majumdar D, Nishiguchi GA, Perez LB, Paris G, Quinn CM, Ramsey T, Sendzik M, Shultz MD, Williams SL, Stams T, Blacklow SC, Acker MG, LaMarche MJ. Dual Allosteric Inhibition of SHP2 Phosphatase. ACS Chem Biol 2018; 13:647-656. [PMID: 29304282 DOI: 10.1021/acschembio.7b00980] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
SHP2 is a cytoplasmic protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell proliferation, differentiation, and survival. Recently, we reported an allosteric mechanism of inhibition that stabilizes the auto-inhibited conformation of SHP2. SHP099 (1) was identified and characterized as a moderately potent, orally bioavailable, allosteric small molecule inhibitor, which binds to a tunnel-like pocket formed by the confluence of three domains of SHP2. In this report, we describe further screening strategies that enabled the identification of a second, distinct small molecule allosteric site. SHP244 (2) was identified as a weak inhibitor of SHP2 with modest thermal stabilization of the enzyme. X-ray crystallography revealed that 2 binds and stabilizes the inactive, closed conformation of SHP2, at a distinct, previously unexplored binding site-a cleft formed at the interface of the N-terminal SH2 and PTP domains. Derivatization of 2 using structure-based design resulted in an increase in SHP2 thermal stabilization, biochemical inhibition, and subsequent MAPK pathway modulation. Downregulation of DUSP6 mRNA, a downstream MAPK pathway marker, was observed in KYSE-520 cancer cells. Remarkably, simultaneous occupation of both allosteric sites by 1 and 2 was possible, as characterized by cooperative biochemical inhibition experiments and X-ray crystallography. Combining an allosteric site 1 inhibitor with an allosteric site 2 inhibitor led to enhanced pharmacological pathway inhibition in cells. This work illustrates a rare example of dual allosteric targeted protein inhibition, demonstrates screening methodology and tactics to identify allosteric inhibitors, and enables further interrogation of SHP2 in cancer and related pathologies.
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Affiliation(s)
- Michelle Fodor
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Edmund Price
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Ping Wang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Hengyu Lu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Andreea Argintaru
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Zhouliang Chen
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Meir Glick
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Huai-Xiang Hao
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Mitsunori Kato
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Robert Koenig
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jonathan R. LaRochelle
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School and Department of Cancer Biology, Dana−Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Gang Liu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Eric McNeill
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Dyuti Majumdar
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Gisele A. Nishiguchi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Lawrence B. Perez
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Gregory Paris
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Christopher M. Quinn
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Timothy Ramsey
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Martin Sendzik
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Michael David Shultz
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Sarah L. Williams
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Travis Stams
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Stephen C. Blacklow
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School and Department of Cancer Biology, Dana−Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Michael G. Acker
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Matthew J. LaMarche
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
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48
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Yu ZH, Zhang ZY. Regulatory Mechanisms and Novel Therapeutic Targeting Strategies for Protein Tyrosine Phosphatases. Chem Rev 2018; 118:1069-1091. [PMID: 28541680 PMCID: PMC5812791 DOI: 10.1021/acs.chemrev.7b00105] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An appropriate level of protein phosphorylation on tyrosine is essential for cells to react to extracellular stimuli and maintain cellular homeostasis. Faulty operation of signal pathways mediated by protein tyrosine phosphorylation causes numerous human diseases, which presents enormous opportunities for therapeutic intervention. While the importance of protein tyrosine kinases in orchestrating the tyrosine phosphorylation networks and in target-based drug discovery has long been recognized, the significance of protein tyrosine phosphatases (PTPs) in cellular signaling and disease biology has historically been underappreciated, due to a large extent to an erroneous assumption that they are largely constitutive and housekeeping enzymes. Here, we provide a comprehensive examination of a number of regulatory mechanisms, including redox modulation, allosteric regulation, and protein oligomerization, that control PTP activity. These regulatory mechanisms are integral to the myriad PTP-mediated biochemical events and reinforce the concept that PTPs are indispensable and specific modulators of cellular signaling. We also discuss how disruption of these PTP regulatory mechanisms can cause human diseases and how these diverse regulatory mechanisms can be exploited for novel therapeutic development.
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Affiliation(s)
- Zhi-Hong Yu
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907
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49
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Xie J, Si X, Gu S, Wang M, Shen J, Li H, Shen J, Li D, Fang Y, Liu C, Zhu J. Allosteric Inhibitors of SHP2 with Therapeutic Potential for Cancer Treatment. J Med Chem 2017; 60:10205-10219. [DOI: 10.1021/acs.jmedchem.7b01520] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jingjing Xie
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan
District, Beijing 100049, China
| | - Xiaojia Si
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer
Feld 270, 69120 Heidelberg, Germany
| | - Shoulai Gu
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
| | - Mingliang Wang
- Department of Natural Products Chemistry, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Jian Shen
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan
District, Beijing 100049, China
| | - Haoyan Li
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan
District, Beijing 100049, China
| | - Jian Shen
- Viva Biotech Ltd. 334 Aidisheng Road, Shanghai 201203, China
| | - Dan Li
- Key Laboratory for
the Genetics of Developmental and Neuropsychiatric Disorders (Ministry
of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanjia Fang
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
| | - Cong Liu
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
| | - Jidong Zhu
- Interdisciplinary
Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201203, China
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50
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Wang WL, Chen XY, Gao Y, Gao LX, Sheng L, Zhu J, Xu L, Ding ZZ, Zhang C, Li JY, Li J, Zhou YB. Benzo[ c ][1,2,5]thiadiazole derivatives: A new class of potent Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2) inhibitors. Bioorg Med Chem Lett 2017; 27:5154-5157. [DOI: 10.1016/j.bmcl.2017.10.059] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 11/16/2022]
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