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Computational Insight into Protein Tyrosine Phosphatase 1B Inhibition: A Case Study of the Combined Ligand- and Structure-Based Approach
2017
Computational and Mathematical Methods in Medicine
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In our work, the way of combined ligand- and structure-based approach was applied to analyze the characteristics of PTP1B enzyme and its interaction with competitive inhibitors. ...
Protein tyrosine phosphatase 1B (PTP1B) is an attractive target for treating cancer, obesity, and type 2 diabetes. ...
To our knowledge, this is the first time that systematical combinations of ligandbased and structure-based approaches provide an insight into PTP1B's active site and the interaction with its ligands by ...
doi:10.1155/2017/4245613
pmid:29441120
pmcid:PMC5758944
fatcat:dg3e6bh5w5ew5okdjzjroiplgi
Chimeric design, synthesis, and biological assays of a new nonpeptide insulin-mimetic vanadium compound to inhibit protein tyrosine phosphatase 1B
2010
Drug Design, Development and Therapy
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Prior to its total synthesis, a new vanadium coordination compound, called TSAG0101, was computationally designed to inhibit the enzyme protein tyrosine phosphatase 1B (PTP1B). ...
In aqueous solution, in presence or absence of sodium citrate as a biologically relevant and ubiquitous chelator, TSAG0101 undergoes neither ligand exchange nor reduction of its central vanadium atom during ...
(SYBYL, MOE); to Prof Dr Reiner Lammers, for in vitro inhibition and activity tests; to PhD Dr Nicolas Lembert, for the extra-pancreatic tests; to Prof Dr H.P.T. ...
doi:10.2147/dddt.s8445
fatcat:vvr2jlmenjgejfuquv4kssotje
Chimeric design, synthesis, and biological assays of a new nonpeptide insulin-mimetic vanadium compound to inhibit protein tyrosine phosphatase 1B
2010
Drug Design, Development and Therapy
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Prior to its total synthesis, a new vanadium coordination compound, called TSAG0101, was computationally designed to inhibit the enzyme protein tyrosine phosphatase 1B (PTP1B). ...
In aqueous solution, in presence or absence of sodium citrate as a biologically relevant and ubiquitous chelator, TSAG0101 undergoes neither ligand exchange nor reduction of its central vanadium atom during ...
(SYBYL, MOE); to Prof Dr Reiner Lammers, for in vitro inhibition and activity tests; to PhD Dr Nicolas Lembert, for the extra-pancreatic tests; to Prof Dr H.P.T. ...
pmid:20957214
pmcid:PMC2948933
fatcat:quna3v4hsfgw7nzmqonspcla2a
Inhibition of Yersinia Tyrosine Phosphatase by Furanyl Salicylate Compounds
2004
Journal of Biological Chemistry
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We used a novel and cost-effective approach, in which leads from a chemical library screening were analyzed and computationally docked into the crystal structure of YopH. ...
To avoid detection and targeting by the immune system, the plague-causing bacterium Yersinia pestis uses a type III secretion system to deliver a set of inhibitory proteins into the cytoplasm of immune ...
DISCUSSION In this study we use an approach to inhibitor design, which can be characterized as a hybrid between traditional high throughput screening and rational design based on the structure of the ...
doi:10.1074/jbc.m413122200
pmid:15615724
fatcat:dnj4bus5avbr3pa32jj3yc7vne
Toward a Molecular Understanding of the Interaction of Dual Specificity Phosphatases with Substrates: Insights from Structure-Based Modeling and High Throughput Screening
2008
Current Medicinal Chemistry
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These studies emphasize the utility of developing computational models and methods that meet the two major challenges currently faced in structure-based in silico design of lead compounds: the conformational ...
Recent experimental and virtual HTS studies, as well as advances in molecular modeling, provide new insights into the potential mechanisms for substrate recognition and binding by this important class ...
Fig. (2) illustrates the catalytic domain of a DSP, cell division cycle 25B (Cdc25B) phosphatase, in comparison to two extensively studied cell signaling enzymes, protein tyrosine phosphatase 1B (PTP1B ...
doi:10.2174/092986708785909003
pmid:18855677
pmcid:PMC2764859
fatcat:pnq7p7p26vgdvmdvtnkpq6clem
Structure-Based Virtual Screening of Protein Tyrosine Phosphatase Inhibitors: Significance, Challenges, and Solutions
2017
Journal of Microbiology and Biotechnology
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Protein tyrosine phosphatases (PTPs) are of prime importance in the process of dephosphorylation and catalyze several biological functions. ...
Pathway or biological activity-based abnormalities in phosphorylation and the type of involved phosphatase influence the outcome, and cause diverse diseases ranging from diabetes, rheumatoid arthritis, ...
An illustrative structure of protein tyrosine phosphatase 1B (PTP1B).
Fig. 3 . 3 Fig. 3. ...
doi:10.4014/jmb.1701.01079
pmid:28238001
fatcat:kxtgoy3kh5dnpksn6dudket4sy
Computer Simulation of TSP1 Inhibition of VEGF–Akt–eNOS: An Angiogenesis Triple Threat
2018
Frontiers in Physiology
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The matricellular protein thrombospondin-1 (TSP1) is a potent inhibitor of angiogenesis. ...
The model further predicts that combination strategy involving depletion of CD47 and inhibition of TSP1 binding to CD47 is necessary for effective recovery of signaling to eNOS. ...
VEGFR2 has a ligand-binding site (L), a tyrosine phosphorylation site (represented as Y1175), and a ligand independent coupling site (c). ...
doi:10.3389/fphys.2018.00644
pmid:29899706
pmcid:PMC5988849
fatcat:s6am5nnekjhnnjnmkpvr23r5ba
Cell signaling regulation by protein phosphorylation: a multivariate, heterogeneous, and context-dependent process
2016
Current Opinion in Biotechnology
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The study of signaling regulation by protein phosphorylation is complicated in part by the sheer scope of the kinome and phosphoproteome, dependence of signaling protein functionality on cellular localization ...
In one example, ligand binding to the extracellular domain of a receptor initiates a network of intracellular biochemical reactions that affect cell phenotypes by modifying gene expression, metabolism, ...
A recent study described a new multiplexed method with absolute quantification and large dynamic range of protein phosphorylation and applied the method to quantify the effects of EGFR inhibition in glioblastoma ...
doi:10.1016/j.copbio.2016.06.005
pmid:27393828
pmcid:PMC4975652
fatcat:xoxs7enrxraizbekanko6oqxdq
Imatinib binding and cKIT inhibition is abrogated by the cKIT kinase domain I missense mutation Val654Ala
2005
Molecular Cancer Therapeutics
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These results highlight some of the structural and functional consequences of the Val 654 Ala mutation in relapsing imatinib-resistant GIST and emphasize the importance of tumor genetics in drug development ...
Several activating mutations in the cKIT receptor tyrosine kinase are associated with the development and progression of gastrointestinal stromal tumors (GIST). ...
Acknowledgments We thank the patients involved in this study and Drs. D. Lagos and S. Henderson for helpful revision of the article. ...
doi:10.1158/1535-7163.mct-05-0070
pmid:16373716
fatcat:snnd7kx4lfdstgxfpdgygua7wa
Structure-based development of target-specific compound libraries
2006
Drug Discovery Today
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A structure-based target-specific library can save time and money by reducing the number of compounds to be experimentally tested, also improving the drug discovery success rate by identifying more-potent ...
Currently, there is a trend towards the construction of receptorstructure-based focused libraries. ...
Acknowledgements The authors thank Hugo O. Villar, from Altoris, for comments and insightful discussions. ...
doi:10.1016/s1359-6446(05)03717-7
pmid:16580603
fatcat:i6o7xom5lbbrrkfr5zxmiwys44
Methods of probing the interactions between small molecules and disordered proteins
2017
Cellular and Molecular Life Sciences (CMLS)
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interactions between disordered proteins; (2) those that inhibit the aberrant aggregation of disordered proteins, and (3) those that lead to binding disordered proteins in their monomeric states. ...
A major bottleneck for the identification of compounds capable of interacting with these proteins and modulating their disease-promoting behaviour is the development of effective techniques to probe such ...
Low resolution
Variable
Protein-tyrosine
phosphatase 1B and
trodusquemine [56]
[114, 115]
Thermal
denaturation
screening
Detection of monomeric binders Non-quantitative
High
Nuclear protein ...
doi:10.1007/s00018-017-2563-4
pmid:28631009
pmcid:PMC5533867
fatcat:z52be5hh3jb5zoqvsz5ahdy7iy
Structural insights into mode of actions of novel natural Mycobacterium protein tyrosine phosphatase B inhibitors
2014
BMC Genomics
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The present study aims at indentifying potent inhibitors of mPTPB by using computational approaches of ligand based molecular modeling and docking studies. ...
Mycobacterium tuberculosis secretes a virulence factor, protein tyrosine phosphatase B (mPTPB) in the cytoplasm of host macrophage which suppresses its natural innate immune response and helps the pathogen ...
Acknowledgements AG is thankful to Jawaharlal Nehru University for usage of all computational facilities. AG is grateful to Department of Science and Technology, Government of India. ...
doi:10.1186/1471-2164-15-s1-s3
pmid:24564493
pmcid:PMC4046716
fatcat:ecf6fryoxjgdbd6kztgbnfmeke
NSC114792, a novel small molecule identified through structure-based computational database screening, selectively inhibits JAK3
2010
Molecular Cancer
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To identify novel small molecule inhibitors of JAK3, we performed structure-based virtual screen using the 3D structure of JAK3 kinase domain and the NCI diversity set of compounds. ...
Human or animals lacking either JAK3 or the common gamma chain (γc) expression display severe combined immunodeficiency disease, indicating the crucial role of JAK3 in T-cell development and the homeostasis ...
Schultz from the NCI Developmental Therapeutics Program for providing the compound of NSC114792. This work was supported by the Children's Cancer Fund (Millwood, NY). ...
doi:10.1186/1476-4598-9-36
pmid:20149240
pmcid:PMC2830973
fatcat:uycwynnoknhnzmmvpum7fa63xi
The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma
2013
Cancer Discovery
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The spectrum of clinical genetic resistance mechanisms to RAF inhibitors and options for salvage therapy are incompletely understood. ...
Besides previously characterized alterations, we discovered a "long tail" of new mitogen-activated protein kinase (MAPK) pathway alterations (MAP2K2, MITF) that confer RAF inhibitor resistance. ...
Authors' Contributions
Acknowledgments The authors thank the patients who were enrolled in this study.
Grant Support ...
doi:10.1158/2159-8290.cd-13-0617
pmid:24265153
pmcid:PMC3947264
fatcat:esv6wt24ubhzrecwp23uwl7nzm
SHP2 Inhibition Influences Therapeutic Response to Tepotinib in Tumors with MET Alterations
2020
iScience
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Alternative signaling pathways potentially diminish the effect of tepotinib monotherapy, and the combination of tepotinib with an SHP2 inhibitor enables the control of tumor growth in cells with MET genetic ...
An Src homology 2 domain-containing phosphatase 2 (SHP2) inhibitor delayed the emergence of tepotinib resistance and synergized with tepotinib in treatment-naive and tepotinib-resistant cells as well as ...
Structural and molecular insight into resistance mechanisms of first generation cMET inhibitors. ACS Med. Chem. Lett. 10, 1322-1327. ...
doi:10.1016/j.isci.2020.101832
pmid:33305187
pmcid:PMC7718487
fatcat:f6up2wzcrfgcbcabluli5gkjza
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