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Boulhissa I, Boucherit H, Chikhi A, Bensegueni A. Docking of T6361 Analogues as Potential Inhibitors of E.coli MurA Followed by ADME-Toxicity Study. Curr Drug Discov Technol 2024; 21:1-8. [PMID: 37929742 DOI: 10.2174/0115701638244582231025110143] [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: 02/01/2023] [Revised: 08/16/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Developing more potent antibacterial agents is one of the most important tasks of scientists in the health field due to the problem of antibiotic resistance. Among the antibiotic targets, we mention MurA (UDP-N-Acetylglucosamine Enolpyruvyl Transferase), which is a key enzyme of peptidoglycan biosynthesis of the bacterial cell wall. OBJECTIVE Our objective was to search for new inhibitors of the bacterial enzyme MurA by docking the analogues of its inhibitor T6361, a derivative of 5-sulfonoxy-anthranilic acid. METHODS 990 analogues of T6361 were docked in the first binding site of E.coli MurA (open form) using the FlexX program, and the ADME-Toxicity profile of the best ones was evaluated by SwissADME and PreADMET web servers. . RESULTS Docking results revealed two T6361 analogues to provide better energy scores than T6361, and have similar interactions with the binding site of E.coli MurA namely,3-{[2-(piperidine-1-carbonyl) phenyl]sulfamoyl}benzoic acid and 3-{[2-(pyrrolidine-1 carbonyl)phenyl]sulfamoyl}benzoic acid. Moreover, the two molecules were found to possess good pharmacokinetics and low toxicity. CONCLUSION We propose two analogues of T6361 as new potential inhibitors of MurA enzyme. Their good ADME-Toxicity profile qualifies them to reach in vitro and in vivo assays as future lead molecules.
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Affiliation(s)
- Ilham Boulhissa
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
| | - Hanane Boucherit
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
- Abdelhafid Boussouf University Center, Mila, Algeria
| | - Abdelouahab Chikhi
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
| | - Abderrahmane Bensegueni
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
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Jassim BA, Lin J, Zhang ZY. PTPN22: Structure, Function, and Developments in Inhibitor Discovery with Applications for Immunotherapy. Expert Opin Drug Discov 2022; 17:825-837. [PMID: 35637605 PMCID: PMC9378720 DOI: 10.1080/17460441.2022.2084607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION While immunotherapy strategies such as immune checkpoint inhibition and adoptive T cell therapy have become commonplace in cancer therapy, they suffer from limitations, including lack of patient response and toxicity. To wield the maximum potential of the immune system, cancer immunotherapy must integrate novel targets and therapeutic strategies with potential to augment clinical efficacy of currently utilized immunotherapies. PTPN22, a member of the protein tyrosine phosphatase (PTP) superfamily that downregulates T cell signaling and proliferation, has recently emerged as a systemically druggable and novel immunotherapy target. AREAS COVERED This review describes the basics of PTPN22 structure and function and provides comprehensive insight into recent advances in small molecule PTPN22 inhibitor development and the immense potential of PTPN22 inhibition to synergize with current immunotherapies. EXPERT OPINION It is apparent that small molecule PTPN22 inhibitors have enormous potential to augment efficacy of current immunotherapy strategies such as checkpoint inhibition and adoptive cell transfer. Nevertheless, several constraints must be overcome before these inhibitors can be applied as useful therapeutics, namely selectivity, potency, and in vivo efficacy.
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Affiliation(s)
- Brenson A Jassim
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, West Lafayette
| | - Jianping Lin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, West Lafayette
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, West Lafayette
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3
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Chen J, Zhao X, Yuan Y, Jing JJ. The expression patterns and the diagnostic/prognostic roles of PTPN family members in digestive tract cancers. Cancer Cell Int 2020; 20:238. [PMID: 32536826 PMCID: PMC7291430 DOI: 10.1186/s12935-020-01315-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/02/2020] [Indexed: 02/06/2023] Open
Abstract
Background Non-receptor protein tyrosine phosphatases (PTPNs) are a set of enzymes involved in the tyrosyl phosphorylation. The present study intended to clarify the associations between the expression patterns of PTPN family members, and diagnosis as well as the prognosis of digestive tract cancers. Methods Oncomine and Ualcan were used to analyze PTPN expressions. Data from The Cancer Genome Atlas (TCGA) were downloaded through UCSC Xena for validation and to explore the relationship of the PTPN expression with diagnosis, clinicopathological parameters and survival of digestive tract cancers. Gene ontology enrichment analysis was conducted using the DAVID database. The gene–gene interaction network was performed by GeneMANIA and the protein–protein interaction (PPI) network was built using STRING portal coupled with Cytoscape. The expression of differentially expressed PTPNs in cancer cell lines were explored using CCLE. Moreover, by histological verification, the expression of four PTPNs in digestive tract cancers were further analyzed. Results Most PTPN family members were associated with digestive tract cancers according to Oncomine, Ualcan and TCGA data. Several PTPN members were differentially expressed in digestive tract cancers. For esophageal carcinoma (ESCA), PTPN1 and PTPN12 levels were correlated with incidence; PTPN20 was associated with poor prognosis. For stomach adenocarcinoma (STAD), PTPN2 and PTPN12 levels were correlated with incidence; PTPN3, PTPN5, PTPN7, PTPN11, PTPN13, PTPN14, PTPN18 and PTPN23 were correlated with pathological grade; PTPN20 expression was related with both TNM stage and N stage; PTPN22 was associated with T stage and pathological grade; decreased expression of PTPN5 and PTPN13 implied worse overall survival of STAD, while elevated PTPN6 expression indicated better prognosis. For colorectal cancer (CRC), PTPN2, PTPN21 and PTPN22 levels were correlated with incidence; expression of PTPN5, PTPN12, and PTPN14 was correlated with TNM stage and N stage; high PTPN5 or PTPN7 expression was associated with increased hazards of death. CCLE analyses showed that in esophagus cancer cell lines, PTPN1, PTPN4 and PTPN12 were highly expressed; in gastric cancer cell lines, PTPN2 and PTPN12 were highly expressed; in colorectal cancer cell lines, PTPN12 was highly expressed while PTPN22 was downregulated. Results of histological verification experiment showed differential expressions of PTPN22 in CRC, and PTPN12 in GC and CRC. Conclusions Members of PTPN family were differentially expressed in digestive tract cancers. Correlations were found between PTPN genes and clinicopathological parameters of patients. Expression of PTPN12 was upregulated in both STAD and CRC, and thus could be used as a diagnostic biomarker. Differential expression of PTPN12 in GC and CRC, and PTPN22 in CRC were presented in our histological verification experiment.
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Affiliation(s)
- Jing Chen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No. 155 North NanjingBei Street, Heping District, Shenyang, 110001 Liaoning People's Republic of China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001 China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001 China
| | - Xu Zhao
- Mathematical Computer Teaching and Research Office, Liaoning Vocational College of Medicine, Shenyang, 110101 China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No. 155 North NanjingBei Street, Heping District, Shenyang, 110001 Liaoning People's Republic of China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001 China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001 China
| | - Jing-Jing Jing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No. 155 North NanjingBei Street, Heping District, Shenyang, 110001 Liaoning People's Republic of China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001 China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001 China
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4
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Beyond the Cell Surface: Targeting Intracellular Negative Regulators to Enhance T cell Anti-Tumor Activity. Int J Mol Sci 2019; 20:ijms20235821. [PMID: 31756921 PMCID: PMC6929154 DOI: 10.3390/ijms20235821] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 02/07/2023] Open
Abstract
It is well established that extracellular proteins that negatively regulate T cell function, such as Cytotoxic T-Lymphocyte-Associated protein 4 (CTLA-4) and Programmed Cell Death protein 1 (PD-1), can be effectively targeted to enhance cancer immunotherapies and Chimeric Antigen Receptor T cells (CAR-T cells). Intracellular proteins that inhibit T cell receptor (TCR) signal transduction, though less well studied, are also potentially useful therapeutic targets to enhance T cell activity against tumor. Four major classes of enzymes that attenuate TCR signaling include E3 ubiquitin kinases such as the Casitas B-lineage lymphoma proteins (Cbl-b and c-Cbl), and Itchy (Itch), inhibitory tyrosine phosphatases, such as Src homology region 2 domain-containing phosphatases (SHP-1 and SHP-2), inhibitory protein kinases, such as C-terminal Src kinase (Csk), and inhibitory lipid kinases such as Src homology 2 (SH2) domain-containing inositol polyphosphate 5-phosphatase (SHIP) and Diacylglycerol kinases (DGKs). This review describes the mechanism of action of eighteen intracellular inhibitory regulatory proteins in T cells within these four classes, and assesses their potential value as clinical targets to enhance the anti-tumor activity of endogenous T cells and CAR-T cells.
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Carmona FD, Martín J. The potential of PTPN22 as a therapeutic target for rheumatoid arthritis. Expert Opin Ther Targets 2018; 22:879-891. [PMID: 30251905 DOI: 10.1080/14728222.2018.1526924] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION PTPN22 encodes a lymphoid-specific tyrosine phosphatase (LYP) that is a master regulator of the immune response. This gene is a major susceptibility factor for a wide range of autoimmune conditions, including rheumatoid arthritis (RA) for which it represents the strongest non-HLA contributor to disease risk. A missense PTPN22 allele (R620W) affecting the protein-protein interaction of LYP with other relevant players was described as the functional variant of the association. This review will focus on the role of PTPN22 in the pathogenic mechanisms underlying RA predisposition and discuss the possibility of developing LYP-based treatment strategies with a potential application in clinical practice. Areas covered: This review covers the literature showing how PTPN22 is implicated in signalling pathways involved in the autoimmune and autoinflammatory processes underlying RA. Insights obtained from studies aimed at developing novel selective LYP suppressors for treating RA are summarized. Expert opinion: Targeting key risk factors during the early steps of the disease may represent a good strategy to accomplish complete disease remission. As cumulating evidences suggest that PTPN22 R620W is a gain-of-function variant, a growing interest in developing LYP inhibitors has arisen. The potential efficacy and possible application of such compounds are discussed.
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Affiliation(s)
- F David Carmona
- a Departamento de Genética e Instituto de Biotecnología , Universidad de Granada , Granada , Spain
| | - Javier Martín
- b Instituto de Parasitología y Biomedicina López-Neyra , Consejo Superior de Investigaciones Científicas, IPBLN-CSIC , Granada , Spain
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6
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Stanford SM, Aleshin AE, Zhang V, Ardecky RJ, Hedrick MP, Zou J, Ganji SR, Bliss MR, Yamamoto F, Bobkov AA, Kiselar J, Liu Y, Cadwell GW, Khare S, Yu J, Barquilla A, Chung TDY, Mustelin T, Schenk S, Bankston LA, Liddington RC, Pinkerton AB, Bottini N. Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase. Nat Chem Biol 2017; 13:624-632. [PMID: 28346406 PMCID: PMC5435566 DOI: 10.1038/nchembio.2344] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 01/06/2017] [Indexed: 11/09/2022]
Abstract
Obesity-associated insulin resistance plays a central role in type 2 diabetes. As such, tyrosine phosphatases that dephosphorylate the insulin receptor (IR) are potential therapeutic targets. The low-molecular-weight protein tyrosine phosphatase (LMPTP) is a proposed IR phosphatase, yet its role in insulin signaling in vivo has not been defined. Here we show that global and liver-specific LMPTP deletion protects mice from high-fat diet-induced diabetes without affecting body weight. To examine the role of the catalytic activity of LMPTP, we developed a small-molecule inhibitor with a novel uncompetitive mechanism, a unique binding site at the opening of the catalytic pocket, and an exquisite selectivity over other phosphatases. This inhibitor is orally bioavailable, and it increases liver IR phosphorylation in vivo and reverses high-fat diet-induced diabetes. Our findings suggest that LMPTP is a key promoter of insulin resistance and that LMPTP inhibitors would be beneficial for treating type 2 diabetes.
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Affiliation(s)
- Stephanie M Stanford
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.,Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Alexander E Aleshin
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Vida Zhang
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.,Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Robert J Ardecky
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Michael P Hedrick
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Jiwen Zou
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Santhi R Ganji
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Matthew R Bliss
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Fusayo Yamamoto
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Andrey A Bobkov
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Janna Kiselar
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yingge Liu
- Institute for Genetic Medicine, University of Southern California, Los Angeles, California, USA
| | - Gregory W Cadwell
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Shilpi Khare
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Jinghua Yu
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Antonio Barquilla
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Thomas D Y Chung
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Tomas Mustelin
- Department of Respiratory, Inflammation and Autoimmunity, MedImmune LLC, Gaithersburg, Maryland, USA
| | - Simon Schenk
- Department of Orthopaedic Surgery and Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Laurie A Bankston
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Robert C Liddington
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Anthony B Pinkerton
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Nunzio Bottini
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.,Department of Medicine, University of California, San Diego, La Jolla, California, USA
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7
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Hou X, Li K, Yu X, Sun JP, Fang H. Protein Flexibility in Docking-Based Virtual Screening: Discovery of Novel Lymphoid-Specific Tyrosine Phosphatase Inhibitors Using Multiple Crystal Structures. J Chem Inf Model 2015; 55:1973-83. [DOI: 10.1021/acs.jcim.5b00344] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xuben Hou
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology
of Natural Products (MOE), School of Pharmacy, ‡Department of Physiology, School
of Medicine, and §Key Laboratory Experimental Teratology of the Ministry of Education
and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Kangshuai Li
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology
of Natural Products (MOE), School of Pharmacy, ‡Department of Physiology, School
of Medicine, and §Key Laboratory Experimental Teratology of the Ministry of Education
and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xiao Yu
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology
of Natural Products (MOE), School of Pharmacy, ‡Department of Physiology, School
of Medicine, and §Key Laboratory Experimental Teratology of the Ministry of Education
and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Jin-peng Sun
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology
of Natural Products (MOE), School of Pharmacy, ‡Department of Physiology, School
of Medicine, and §Key Laboratory Experimental Teratology of the Ministry of Education
and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Hao Fang
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology
of Natural Products (MOE), School of Pharmacy, ‡Department of Physiology, School
of Medicine, and §Key Laboratory Experimental Teratology of the Ministry of Education
and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
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8
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Hou X, Li R, Li K, Yu X, Sun JP, Fang H. Fast Identification of Novel Lymphoid Tyrosine Phosphatase Inhibitors Using Target–Ligand Interaction-Based Virtual Screening. J Med Chem 2014; 57:9309-22. [DOI: 10.1021/jm500692u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Xuben Hou
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Rong Li
- Key
Laboratory Experimental Teratology of the Ministry of Education and
Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Kangshuai Li
- Department
of Physiology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xiao Yu
- Department
of Physiology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Jin-Peng Sun
- Key
Laboratory Experimental Teratology of the Ministry of Education and
Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Hao Fang
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
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Ghattas MA, Atatreh N, Bichenkova EV, Bryce RA. Protein tyrosine phosphatases: Ligand interaction analysis and optimisation of virtual screening. J Mol Graph Model 2014; 52:114-23. [PMID: 25038507 DOI: 10.1016/j.jmgm.2014.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/23/2014] [Accepted: 06/26/2014] [Indexed: 11/28/2022]
Abstract
Docking-based virtual screening is an established component of structure-based drug discovery. Nevertheless, scoring and ranking of computationally docked ligand libraries still suffer from many false positives. Identifying optimal docking parameters for a target protein prior to virtual screening can improve experimental hit rates. Here, we examine protocols for virtual screening against the important but challenging class of drug target, protein tyrosine phosphatases. In this study, common interaction features were identified from analysis of protein-ligand binding geometries of more than 50 complexed phosphatase crystal structures. It was found that two interactions were consistently formed across all phosphatase inhibitors: (1) a polar contact with the conserved arginine residue, and (2) at least one interaction with the P-loop backbone amide. In order to investigate the significance of these features on phosphatase-ligand binding, a series of seeded virtual screening experiments were conducted on three phosphatase enzymes, PTP1B, Cdc25b and IF2. It was observed that when the conserved arginine and P-loop amide interactions were used as pharmacophoric constraints during docking, enrichment of the virtual screen significantly increased in the three studied phosphatases, by up to a factor of two in some cases. Additionally, the use of such pharmacophoric constraints considerably improved the ability of docking to predict the inhibitor's bound pose, decreasing RMSD to the crystallographic geometry by 43% on average. Constrained docking improved enrichment of screens against both open and closed conformations of PTP1B. Incorporation of an ordered water molecule in PTP1B screening was also found to generally improve enrichment. The knowledge-based computational strategies explored here can potentially inform structure-based design of new phosphatase inhibitors using docking-based virtual screening.
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Affiliation(s)
- Mohammad A Ghattas
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain 64141, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain 64141, United Arab Emirates
| | - Elena V Bichenkova
- Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Richard A Bryce
- Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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Zheng J, Petersen F, Yu X. The role of PTPN22 in autoimmunity: learning from mice. Autoimmun Rev 2013; 13:266-71. [PMID: 24189282 DOI: 10.1016/j.autrev.2013.10.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 10/24/2013] [Indexed: 02/07/2023]
Abstract
Protein tyrosine phosphatase nonreceptor 22 (PTPN22) represents a strong susceptibility gene which is shared by many autoimmune diseases. Exploring the mechanism behind this association could help to understand their pathogenesis as well as to identify novel therapeutical targets. Recently, multiple mouse models including knock-out, knock-in, knock-down and transgenic mice were generated to delineate PTPN22s function in this context. Depending on the genetic background, mouse PTPN22_619W mutation results in spontaneous autoimmunity, essentially replicating the risk effect of the PTPN22_620W in human autoimmune diseases. Furthermore, findings from mouse models shed new light on both cellular as well as molecular mechanisms of the effect of PTPN22 on adaptive and innate immunity. Here we review recently emerged evidence of the interconnection between mouse PTPN22 and autoimmunity. We also discuss the consistence and discrepancy between findings derived from human and mouse studies.
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Affiliation(s)
- Junfeng Zheng
- Laboratory of Autoimmunity, The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China
| | - Frank Petersen
- Priority Area Asthma and Allergy, Research Center Borstel, 23845, Borstel, Germany
| | - Xinhua Yu
- Laboratory of Autoimmunity, The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China; Priority Area Asthma and Allergy, Research Center Borstel, 23845, Borstel, Germany.
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11
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Chen Z, Zhang H, Xia B, Wang P, Jiang T, Song M, Wu J. Association of PTPN22 gene (rs2488457) polymorphism with ulcerative colitis and high levels of PTPN22 mRNA in ulcerative colitis. Int J Colorectal Dis 2013; 28:1351-8. [PMID: 23456301 DOI: 10.1007/s00384-013-1671-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/17/2013] [Indexed: 02/04/2023]
Abstract
PURPOSE Our aims were to evaluate protein tyrosine phosphatase nonreceptor type 22 (PTPN22) gene polymorphisms in ulcerative colitis (UC) and explore PTPN22 mRNA levels in colonic biopsies of UC patients in central China. METHODS A total of 165 Chinese UC patients and 300 healthy controls were enrolled in this study. PTPN22 -1123G/C, +1858C/T, and +788G/A polymorphisms were genotyped by PCR-restriction fragment length polymorphism method. PTPN22 mRNA expressions in colonic biopsies and serum C-reactive protein (CRP) levels were determined by quantitative PCR and immunonephelometry, respectively. RESULTS The frequency of C carrier was higher in UC patients than in healthy controls (66.7 vs. 53.3%, P = 0.005, odds ratios = 1.75, 95% CI 1.18-2.60) and associated with extensive colitis (P = 0.029). PTPN22 mRNA levels were elevated in UC patients than in healthy controls (P < 0.001). Among UC patients, PTPN22 mRNA expression levels were higher in biopsies of inflamed colonic tissue compared with noninflamed tissue (P < 0.001) and were correlated with CRP levels (r = 0.578, P < 0.001). PTPN22 mRNA expression levels were elevated in extensive colitis compared to proctitis (P = 0.008) and to left-sided colitis (P = 0.029) and were higher in moderate and severe disease than in mild disease (P = 0.005). CONCLUSIONS Our study showed the potential association between PTPN22 -1123G/C polymorphism and UC in central China. PTPN22 mRNA levels were highly expressed in UC, especially in active disease, and were correlated with CRP levels, disease location, and disease severity in UC patients.
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Affiliation(s)
- Zhitao Chen
- Department of Gastroenterology and Central Laboratory, The Central Hospital of Wuhan, Sheng Li Street 26, Wuhan, 430014, Hubei Province, People's Republic of China
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12
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Integrating virtual and biochemical screening for protein tyrosine phosphatase inhibitor discovery. Methods 2013; 65:219-28. [PMID: 23969317 DOI: 10.1016/j.ymeth.2013.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 12/14/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) represent an important class of enzymes that mediate signal transduction and control diverse aspects of cell behavior. The importance of their activity is exemplified by their significant contribution to disease etiology with over half of all human PTP genes implicated in at least one disease. Small molecule inhibitors targeting individual PTPs are important biological tools, and are needed to fully characterize the function of these enzymes. Moreover, potent and selective PTP inhibitors hold the promise to transform the treatment of many diseases. While numerous methods exist to develop PTP-directed small molecules, we have found that complimentary use of both virtual (in silico) and biochemical (in vitro) screening approaches expedite compound identification and drug development. Here, we summarize methods pertinent to our work and others. Focusing on specific challenges and successes we have experienced, we discuss the considerable caution that must be taken to avoid enrichment of inhibitors that function by non-selective oxidation. We also discuss the utility of using "open" PTP structures to identify active-site directed compounds, a rather unconventional choice for virtual screening. When integrated closely, virtual and biochemical screening can be used in a productive workflow to identify small molecules targeting PTPs.
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13
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He Y, Liu S, Menon A, Stanford S, Oppong E, Gunawan AM, Wu L, Wu DJ, Barrios AM, Bottini N, Cato ACB, Zhang ZY. A potent and selective small-molecule inhibitor for the lymphoid-specific tyrosine phosphatase (LYP), a target associated with autoimmune diseases. J Med Chem 2013; 56:4990-5008. [PMID: 23713581 PMCID: PMC3711248 DOI: 10.1021/jm400248c] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Lymphoid-specific tyrosine phosphatase (LYP), a member of the protein tyrosine phosphatase (PTP) family of signaling enzymes, is associated with a broad spectrum of autoimmune diseases. Herein we describe our structure-based lead optimization efforts within a 6-hydroxy-benzofuran-5-carboxylic acid series culminating in the identification of compound 8b, a potent and selective inhibitor of LYP with a K(i) value of 110 nM and more than 9-fold selectivity over a large panel of PTPs. The structure of LYP in complex with 8b was obtained by X-ray crystallography, providing detailed information about the molecular recognition of small-molecule ligands binding LYP. Importantly, compound 8b possesses highly efficacious cellular activity in both T- and mast cells and is capable of blocking anaphylaxis in mice. Discovery of 8b establishes a starting point for the development of clinically useful LYP inhibitors for treating a wide range of autoimmune disorders.
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Affiliation(s)
- Yantao He
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Sijiu Liu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Ambili Menon
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von- Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Stephanie Stanford
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Emmanuel Oppong
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von- Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Andrea M. Gunawan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Li Wu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Dennis J. Wu
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Amy M. Barrios
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Nunzio Bottini
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Andrew C. B. Cato
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von- Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Zhong-Yin Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
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14
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Tautz L, Critton DA, Grotegut S. Protein tyrosine phosphatases: structure, function, and implication in human disease. Methods Mol Biol 2013; 1053:179-221. [PMID: 23860656 DOI: 10.1007/978-1-62703-562-0_13] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein tyrosine phosphorylation is a key regulatory mechanism in eukaryotic cell physiology. Aberrant expression or function of protein tyrosine kinases and protein tyrosine phosphatases can lead to serious human diseases, including cancer, diabetes, as well as cardiovascular, infectious, autoimmune, and neuropsychiatric disorders. Here, we give an overview of the protein tyrosine phosphatase superfamily with its over 100 members in humans. We review their structure, function, and implications in human diseases, and discuss their potential as novel drug targets, as well as current challenges and possible solutions to developing therapeutics based on these enzymes.
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Affiliation(s)
- Lutz Tautz
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
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15
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Martin KR, Narang P, Xu Y, Kauffman AL, Petit J, Xu HE, Meurice N, MacKeigan JP. Identification of small molecule inhibitors of PTPσ through an integrative virtual and biochemical approach. PLoS One 2012. [PMID: 23185579 PMCID: PMC3502291 DOI: 10.1371/journal.pone.0050217] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
PTPσ is a dual-domain receptor type protein tyrosine phosphatase (PTP) with physiologically important functions which render this enzyme an attractive biological target. Specifically, loss of PTPσ has been shown to elicit a number of cellular phenotypes including enhanced nerve regeneration following spinal cord injury (SCI), chemoresistance in cultured cancer cells, and hyperactive autophagy, a process critical to cell survival and the clearance of pathological aggregates in neurodegenerative diseases. Owing to these functions, modulation of PTPσ may provide therapeutic value in a variety of contexts. Furthermore, a small molecule inhibitor would provide utility in discerning the cellular functions and substrates of PTPσ. To develop such molecules, we combined in silico modeling with in vitro phosphatase assays to identify compounds which effectively inhibit the enzymatic activity of PTPσ. Importantly, we observed that PTPσ inhibition was frequently mediated by oxidative species generated by compounds in solution, and we further optimized screening conditions to eliminate this effect. We identified a compound that inhibits PTPσ with an IC50 of 10 µM in a manner that is primarily oxidation-independent. This compound favorably binds the D1 active site of PTPσ in silico, suggesting it functions as a competitive inhibitor. This compound will serve as a scaffold structure for future studies designed to build selectivity for PTPσ over related PTPs.
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Affiliation(s)
- Katie R. Martin
- Laboratory of Systems Biology, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
| | - Pooja Narang
- Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Yong Xu
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
| | - Audra L. Kauffman
- Laboratory of Systems Biology, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
| | - Joachim Petit
- Mayo Clinic, Scottsdale, Arizona, United States of America
| | - H. Eric Xu
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
| | | | - Jeffrey P. MacKeigan
- Laboratory of Systems Biology, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
- * E-mail:
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16
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He R, Zeng LF, He Y, Zhang S, Zhang ZY. Small molecule tools for functional interrogation of protein tyrosine phosphatases. FEBS J 2012; 280:731-50. [PMID: 22816879 DOI: 10.1111/j.1742-4658.2012.08718.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The importance of protein tyrosine phosphatases (PTPs) in the regulation of cellular signalling is well established. Malfunction of PTP activity is also known to be associated with cancer, metabolic syndromes and autoimmune disorders, as well as neurodegenerative and infectious diseases. However, a detailed understanding of the roles played by the PTPs in normal physiology and in pathogenic conditions has been hampered by the absence of PTP-specific small molecule agents. In addition, the therapeutic benefits of modulating this target class are underexplored as a result of a lack of suitable chemical probes. Potent and specific PTP inhibitors could significantly facilitate functional analysis of the PTPs in complex cellular signal transduction pathways and may constitute valuable therapeutics in the treatment of several human diseases. We highlight the current challenges to and opportunities for developing PTP-specific small molecule agents. We also review available selective small molecule inhibitors developed for a number of PTPs, including PTP1B, TC-PTP, SHP2, lymphoid-specific tyrosine phosphatase, haematopoietic protein tyrosine phosphatase, CD45, PTPβ, PTPγ, PTPRO, Vaccinia H1-related phosphatase, mitogen-activated protein kinase phosphatase-1, mitogen-activated protein kinase phosphatase-3, Cdc25, YopH, mPTPA and mPTPB.
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Affiliation(s)
- Rongjun He
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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17
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Neves MAC, Totrov M, Abagyan R. Docking and scoring with ICM: the benchmarking results and strategies for improvement. J Comput Aided Mol Des 2012; 26:675-86. [PMID: 22569591 DOI: 10.1007/s10822-012-9547-0] [Citation(s) in RCA: 233] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 01/21/2012] [Indexed: 02/05/2023]
Abstract
Flexible docking and scoring using the internal coordinate mechanics software (ICM) was benchmarked for ligand binding mode prediction against the 85 co-crystal structures in the modified Astex data set. The ICM virtual ligand screening was tested against the 40 DUD target benchmarks and 11-target WOMBAT sets. The self-docking accuracy was evaluated for the top 1 and top 3 scoring poses at each ligand binding site with near native conformations below 2 Å RMSD found in 91 and 95% of the predictions, respectively. The virtual ligand screening using single rigid pocket conformations provided the median area under the ROC curves equal to 69.4 with 22.0% true positives recovered at 2% false positive rate. Significant improvements up to ROC AUC = 82.2 and ROC((2%)) = 45.2 were achieved following our best practices for flexible pocket refinement and out-of-pocket binding rescore. The virtual screening can be further improved by considering multiple conformations of the target.
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Affiliation(s)
- Marco A C Neves
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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18
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Rhee I, Veillette A. Protein tyrosine phosphatases in lymphocyte activation and autoimmunity. Nat Immunol 2012; 13:439-47. [PMID: 22513334 DOI: 10.1038/ni.2246] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lymphocyte activation must be tightly regulated to ensure sufficient immunity to pathogens and prevent autoimmunity. Protein tyrosine phosphatases (PTPs) serve critical roles in this regulation by controlling the functions of key receptors and intracellular signaling molecules in lymphocytes. In some cases, PTPs inhibit lymphocyte activation, whereas in others they promote it. Here we discuss recent progress in elucidating the roles and mechanisms of action of PTPs in lymphocyte activation. We also review the accumulating evidence that genetic alterations in PTPs are involved in human autoimmunity.
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Affiliation(s)
- Inmoo Rhee
- Laboratory of Molecular Oncology, Clinical Research Institute of Montréal, Montréal, Québec, Canada
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19
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Vang T, Liu WH, Delacroix L, Wu S, Vasile S, Dahl R, Yang L, Musumeci L, Francis D, Landskron J, Tasken K, Tremblay ML, Lie BA, Page R, Mustelin T, Rahmouni S, Rickert RC, Tautz L. LYP inhibits T-cell activation when dissociated from CSK. Nat Chem Biol 2012; 8:437-46. [PMID: 22426112 PMCID: PMC3329573 DOI: 10.1038/nchembio.916] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 01/27/2012] [Indexed: 01/17/2023]
Abstract
Lymphoid tyrosine phosphatase (LYP) and C-terminal Src kinase (CSK) are negative regulators of signaling mediated through the T cell antigen receptor (TCR) and are thought to act in a cooperative manner when forming a complex. Here, we studied the spatio-temporal dynamics of the LYP/CSK complex in T cells. We demonstrate that dissociation of this complex is necessary for recruitment of LYP to the plasma membrane, where it down-modulates TCR signaling. Development of a potent and selective chemical probe of LYP confirmed that LYP inhibits T cell activation when removed from CSK. Our findings may explain the reduced TCR-mediated signaling associated with a single nucleotide polymorphism, which confers increased risk for certain autoimmune diseases, including type 1 diabetes and rheumatoid arthritis, and results in expression of a LYP allele that is unable to bind CSK. Our compound also represents a starting point for the development of a LYP-based treatment of autoimmunity.
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Affiliation(s)
- Torkel Vang
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, USA
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20
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Braithwaite SP, Stock JB, Lombroso PJ, Nairn AC. Protein phosphatases and Alzheimer's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 106:343-79. [PMID: 22340724 PMCID: PMC3739963 DOI: 10.1016/b978-0-12-396456-4.00012-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Alzheimer's Disease (AD) is characterized by progressive loss of cognitive function, linked to marked neuronal loss. Pathological hallmarks of the disease are the accumulation of the amyloid-β (Aβ) peptide in the form of amyloid plaques and the intracellular formation of neurofibrillary tangles (NFTs). Accumulating evidence supports a key role for protein phosphorylation in both the normal and pathological actions of Aβ as well as the formation of NFTs. NFTs contain hyperphosphorylated forms of the microtubule-binding protein tau, and phosphorylation of tau by several different kinases leads to its aggregation. The protein kinases involved in the generation and/or actions of tau or Aβ are viable drug targets to prevent or alleviate AD pathology. However, it has also been recognized that the protein phosphatases that reverse the actions of these protein kinases are equally important. Here, we review recent advances in our understanding of serine/threonine and tyrosine protein phosphatases in the pathology of AD.
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21
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Brunschweiger A, Hall J. A decade of the human genome sequence--how does the medicinal chemist benefit? ChemMedChem 2011; 7:194-203. [PMID: 22170741 DOI: 10.1002/cmdc.201100498] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Indexed: 12/11/2022]
Abstract
Many have claimed that the sequencing of the human genome has failed to deliver the promised new era of drug discovery and development. Here, we argue that in fact, the availability of the human genome sequence and the genomics technologies that resulted from those research efforts have had a major impact on drug discovery. Medicinal chemists are actively using the data gleaned from structural genomics projects over the past decade to design more selective and more effective drug candidates. For example, large superfamilies of related enzymes, such as the kinome, proteome, proteasome, transportome, identified because of the sequencing of the human genome represent a huge number of potential drug targets. Ten years on, we're able to design multitarget drugs where the selectivity for a certain subgroup of receptors can lead to increased efficacy rather than the side effects traditionally associated with "off-targets". New trends and discoveries in biomedical research are notoriously slow to show their value, and this is also true for genomics technologies. However, the examples we've selected show that these are firmly set in the drug-discovery process, and without the human genome sequence, a number of current clinical candidates and promising drug leads would not have been possible.
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Affiliation(s)
- Andreas Brunschweiger
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Wolfgang-Pauli-Str. 10, 8093 Zurich, Switzerland
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22
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Anis SK, Abdel Ghany EA, Mostafa NO, Ali AA. The role of PTPN22 gene polymorphism in childhood immune thrombocytopenic purpura. Blood Coagul Fibrinolysis 2011; 22:521-5. [DOI: 10.1097/mbc.0b013e328347b064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Protein tyrosine phosphatases as drug targets: strategies and challenges of inhibitor development. Future Med Chem 2011; 2:1563-76. [PMID: 21426149 DOI: 10.4155/fmc.10.241] [Citation(s) in RCA: 217] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Several 'classical' protein tyrosine phosphatases are attractive therapeutic targets, including PTP1B for obesity and Type II diabetes; SHP2 for cancer and Lyp for rheumatoid arthritis. Progress has been made in identifying a broad range of chemically distinct inhibitors; however, developing selective and cell-permeable clinically useful compounds has proved challenging. Here the ongoing challenges and recent significant advances in the field are reviewed. Key novel compounds are highlighted and a perspective on the future of phosphatase inhibitor development is presented.
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24
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Stanford SM, Krishnamurthy D, Falk MD, Messina R, Debnath B, Li S, Liu T, Kazemi R, Dahl R, He Y, Yu X, Chan AC, Zhang ZY, Barrios AM, Woods VL, Neamati N, Bottini N. Discovery of a novel series of inhibitors of lymphoid tyrosine phosphatase with activity in human T cells. J Med Chem 2011; 54:1640-54. [PMID: 21341673 PMCID: PMC3086468 DOI: 10.1021/jm101202j] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The lymphoid tyrosine phosphatase LYP, encoded by the PTPN22 gene, is a critical regulator of signaling in T cells and recently emerged as a candidate target for therapy of autoimmune diseases. Here, by library screening, we identified a series of noncompetitive inhibitors of LYP that showed activity in primary T cells. Kinetic analysis confirmed that binding of the compounds to the phosphatase is nonmutually exclusive with respect to a known bidentate competitive inhibitor. The mechanism of action of the lead inhibitor compound 4e was studied by a combination of hydrogen/deuterium-exchange mass spectrometry and molecular modeling. The results suggest that the inhibitor interacts critically with a hydrophobic patch located outside the active site of the phosphatase. Targeting of secondary allosteric sites is viewed as a promising yet unexplored approach to develop pharmacological inhibitors of protein tyrosine phosphatases. Our novel scaffold could be a starting point to attempt development of "nonactive site" anti-LYP pharmacological agents.
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Affiliation(s)
- Stephanie M. Stanford
- Institute for Genetic Medicine, University of Southern California, Los Angeles, California 90033, United States
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, United States
| | - Divya Krishnamurthy
- Institute for Genetic Medicine, University of Southern California, Los Angeles, California 90033, United States
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Matthew D. Falk
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, United States
| | - Rossella Messina
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, United States
| | - Bikash Debnath
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90033, United States
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Tong Liu
- Department of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Roza Kazemi
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90033, United States
| | - Russell Dahl
- CPCCG, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - Yantao He
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana 46202, United States
| | - Xiao Yu
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana 46202, United States
| | - Andrew C. Chan
- Department of Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Zhong-Yin Zhang
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana 46202, United States
| | - Amy M. Barrios
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Virgil L. Woods
- Department of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Nouri Neamati
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90033, United States
| | - Nunzio Bottini
- Institute for Genetic Medicine, University of Southern California, Los Angeles, California 90033, United States
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, United States
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25
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Vang T, Xie Y, Liu WH, Vidović D, Liu Y, Wu S, Smith DH, Rinderspacher A, Chung C, Gong G, Mustelin T, Landry DW, Rickert RC, Schürer SC, Deng SX, Tautz L. Inhibition of lymphoid tyrosine phosphatase by benzofuran salicylic acids. J Med Chem 2010; 54:562-71. [PMID: 21190368 DOI: 10.1021/jm101004d] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The lymphoid tyrosine phosphatase (Lyp, PTPN22) is a critical negative regulator of T cell antigen receptor (TCR) signaling. A single-nucleotide polymorphism (SNP) in the ptpn22 gene correlates with the incidence of various autoimmune diseases, including type 1 diabetes, rheumatoid arthritis, and systemic lupus erythematosus. Since the disease-associated allele is a more potent inhibitor of TCR signaling, specific Lyp inhibitors may become valuable in treating autoimmunity. Using a structure-based approach, we synthesized a library of 34 compounds that inhibited Lyp with IC(50) values between 0.27 and 6.2 μM. A reporter assay was employed to screen for compounds that enhanced TCR signaling in cells, and several inhibitors displayed a dose-dependent, activating effect. Subsequent probing for Lyp's direct physiological targets by immunoblot analysis confirmed the ability of the compounds to inhibit Lyp in T cells. Selectivity profiling against closely related tyrosine phosphatases and in silico docking studies with the crystal structure of Lyp yielded valuable information for the design of Lyp-specific compounds.
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Affiliation(s)
- Torkel Vang
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
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26
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Walton ZE, Bishop AC. Target-specific control of lymphoid-specific protein tyrosine phosphatase (Lyp) activity. Bioorg Med Chem 2010; 18:4884-91. [PMID: 20594861 DOI: 10.1016/j.bmc.2010.06.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 06/01/2010] [Accepted: 06/07/2010] [Indexed: 01/14/2023]
Abstract
Lymphoid-specific protein tyrosine phosphatase (Lyp), a member of the protein tyrosine phosphatase (PTP) superfamily of enzymes, is an important mediator of human-leukocyte signaling. Lyp has also emerged as a potential anti-autoimmune therapeutic target, owing to the association of a Lyp-activating mutation with an array of autoimmune disorders. Toward the goal of generating a selective inhibitor of Lyp activity that could be used for investigating Lyp's roles in cell signaling and autoimmune-disease progression, here we report that Lyp's PTP domain can be readily sensitized to target-specific inhibition by a cell-permeable small molecule. Insertion of a tetracysteine-motif-containing peptide at a conserved position in Lyp's catalytic domain generated a mutant enzyme (Lyp-CCPGCC) that retains activity comparable to that of wild-type Lyp in the absence of added ligand. Upon addition of a tetracysteine-targeting biarsenical compound (FlAsH), however, the activity of the Lyp-CCPGCC drops dramatically, as assayed with either small-molecule or phosphorylated-peptide PTP substrates. We show that FlAsH-induced Lyp-CCPGCC inhibition is potent, specific, rapid, and independent of the nature of the PTP substrate used in the inhibition assay. Moreover, we show that FlAsH can be used to specifically target overexpressed Lyp-CCPGCC in a complex proteomic mixture. Since the mammalian-cell permeability of FlAsH is well established, it is likely that FlAsH-mediated inhibition of Lyp-CCPGCC will be useful for specifically targeting Lyp activity in engineered leukocytes and autoimmune-disease models.
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Affiliation(s)
- Zandra E Walton
- Amherst College, Department of Chemistry, Amherst, MA 01002, United States
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27
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Mukherjee P, Desai P, Zhou YD, Avery M. Targeting the BH3 Domain Mediated Protein−Protein Interaction of Bcl-xL through Virtual Screening. J Chem Inf Model 2010; 50:906-23. [DOI: 10.1021/ci1000373] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Prasenjit Mukherjee
- Department of Medicinal Chemistry and Department of Pharmacognosy, School of Pharmacy, University of Mississippi, University, Mississippi 38677
| | - Prashant Desai
- Department of Medicinal Chemistry and Department of Pharmacognosy, School of Pharmacy, University of Mississippi, University, Mississippi 38677
| | - Yu-Dong Zhou
- Department of Medicinal Chemistry and Department of Pharmacognosy, School of Pharmacy, University of Mississippi, University, Mississippi 38677
| | - Mitchell Avery
- Department of Medicinal Chemistry and Department of Pharmacognosy, School of Pharmacy, University of Mississippi, University, Mississippi 38677
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28
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Krüger DM, Evers A. Comparison of structure- and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors. ChemMedChem 2010; 5:148-58. [PMID: 19908272 DOI: 10.1002/cmdc.200900314] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Structure- and ligand-based virtual-screening methods (docking, 2D- and 3D-similarity searching) were analysed for their effectiveness in virtual screening against four different targets: angiotensin-converting enzyme (ACE), cyclooxygenase 2 (COX-2), thrombin and human immunodeficiency virus 1 (HIV-1) protease. The relative performance of the tools was compared by examining their ability to recognise known active compounds from a set of actives and nonactives. Furthermore, we investigated whether the application of different virtual-screening methods in parallel provides complementary or redundant hit lists. Docking was performed with GOLD, Glide, FlexX and Surflex. The obtained docking poses were rescored by using nine different scoring functions in addition to the scoring functions implemented as objective functions in the docking algorithms. Ligand-based virtual screening was done with ROCS (3D-similarity searching), Feature Trees and Scitegic Functional Fingerprints (2D-similarity searching). The results show that structure- and ligand-based virtual-screening methods provide comparable enrichments in detecting active compounds. Interestingly, the hit lists that are obtained from different virtual-screening methods are generally highly complementary. These results suggest that a parallel application of different structure- and ligand-based virtual-screening methods increases the chance of identifying more (and more diverse) active compounds from a virtual-screening campaign.
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Affiliation(s)
- Dennis M Krüger
- Institut für pharmazeutische und medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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29
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Stanford SM, Mustelin TM, Bottini N. Lymphoid tyrosine phosphatase and autoimmunity: human genetics rediscovers tyrosine phosphatases. Semin Immunopathol 2010; 32:127-36. [PMID: 20204370 DOI: 10.1007/s00281-010-0201-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Accepted: 01/28/2010] [Indexed: 01/22/2023]
Abstract
A relatively large number of protein tyrosine phosphatases (PTPs) are known to regulate signaling through the T cell receptor (TCR). Recent human genetics studies have shown that several of these PTPs are encoded by major autoimmunity genes. Here, we will focus on the lymphoid tyrosine phosphatase (LYP), a critical negative modulator of TCR signaling encoded by the PTPN22 gene. The functional analysis of autoimmune-associated PTPN22 genetic variants suggests that genetic variability of TCR signal transduction contributes to the pathogenesis of autoimmunity in humans.
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Affiliation(s)
- Stephanie M Stanford
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
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