Design of specific inhibitors of the protein tyrosine phosphatase SHP-2 by virtual screening and core hopping method

References

• ChanG, KalaitzidisD, NeelBG. The tyrosine phosphatase Shp2 (PTPN11) in cancer. Cancer Metastasis Rev. 2008;27(179):192.
   Google Scholar
• MohiMG, NeelBG. The role of Shp2 (PTPN11) in cancer. Curr Opin Genet Dev. 2007;2007(17):23–30.
   Web of Science ®Google Scholar
• Vercauteren M, Remy E, Devaux C, Dautreaux B, Henry JP, Bauer F, Mulder P, Hooft van Huijsduijnen R, Bombrun A, Thuillez C, Richard V. Improvement of peripheral endothelial dysfunction by protein tyrosine phosphatase inhibitors in heart failure. Circulation. 2006;114:2498–2507.
   Google Scholar
• NeelBG, GuH, PaoL. The ‘Shp'ing news: SH2 domain-containing tyrosine phosphatases in cell signaling. Trends Biochem Sci. 2003;28:284–293.
   PubMed Web of Science ®Google Scholar
• TonksNK. Protein tyrosine phosphatases: from genes, to function, to disease. Nat Rev Mol Cell Biol. 2006;7:833–846.
   PubMed Web of Science ®Google Scholar
• QuCK. Role of the SHP-2 tyrosine phosphatase in cytokine-induced signaling and cellular response. Biochim Biophys Acta. 2002;1592:297–301.
   PubMed Web of Science ®Google Scholar
• ChanRJ, FengGS. PTPN11 is the first identified proto-oncogene that encodes a tyrosine phosphatase. Blood. 2007;109:862–867.
   PubMed Web of Science ®Google Scholar
• TartagliaM, NiemeyerCM, FragaleA, SongX, BuechnerJ, JungA, HählenK, HasleH, LichtJD, GelbBD. Somatic mutations in PTPN11 in juvenile myelomonocytic leukemia, myelodysplastic syndromes and acute myeloid leukemia. Nat Genet. 2003;34:148–150.
   PubMed Web of Science ®Google Scholar
• LohML, VattikutiS, SchubbertS, ReynoldsMG, CarlsonE, LieuwKH, ChengJW, LeeCM, StokoeD, BonifasJM, CurtissNP, GotlibJ, MeshinchiS, Le BeauMM, EmanuelPD, ShannonKM. Mutations in PTPN11 implicate the SHP-2 phosphatase in leukemogenesis. Blood. 2004;103:2325–2331.
   PubMed Web of Science ®Google Scholar
• TartagliaM, MehlerEL, GoldbergR, ZampinoG, BrunnerHG, KremerH, vander BurgtI, CrosbyAH, IonA, JefferyS, KalidasK, PattonMA, KucherlapatiRS, GelbBD. Mutations in PTPN11, encoding the protein tyrosine phosphatase SHP-2, cause Noonan syndrome. Nat Genet. 2001:465–468.
   PubMed Web of Science ®Google Scholar
• ChenL, SungSS, YipML, LawrenceHR, RenY, GuidaWC, SebtiSM, LawrenceNJ, WuJ. Discovery of a novel shp2 protein tyrosine phosphatase inhibitor. Mol Pharmacol. 2006;70:562–570.
   PubMed Web of Science ®Google Scholar
• YuWM, GuvenchO, MackerellAD, QuCK. Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay. J Med Chem. 2008;51:7396–7404.
   PubMed Web of Science ®Google Scholar
• EckMJ, PluskeyS, TrübT, HarrisonSC, ShoelsonSE. Spatial constraints on the recognition of phosphoproteins by the tandem SH2 domains of the phosphatase SH-PTP2. Nature. 1996;379:277–280.
   PubMed Web of Science ®Google Scholar
• HofP, PluskeyS, Dhe-PaganonS, EckMJ, ShoelsonSE. Crystal structure of the tyrosine phosphatase SHP-2. Cell. 1998;92:441–450.
   PubMed Web of Science ®Google Scholar
• BarfordD, NeelBG. Revealing mechanisms for SH2 domain mediated regulation of the protein tyrosine phosphatase SHP-2. Structure. 1998;6:249–254.
   PubMed Web of Science ®Google Scholar
• Schrodinger Suite. Core hopping. New York: Schrödinger, LLC; 2009.
   Google Scholar
• WangJF, ChouKC. Insights from modeling the 3D structure of New Delhi metallo-beta-lactamse and its binding interactions with antibiotic drugs. PLoS One. 2011;6:e18414.
   PubMed Web of Science ®Google Scholar
• ChouKC, WeiDQ, ZhongWZ. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochem Biophys Res Commun. 2003;17:148–151.
   Web of Science ®Google Scholar
• Dea-AyuelaMA, Pérez-CastilloY, Meneses-MarcelA, UbeiraFM, Bolas-FernándezF, ChouKC, González-DíazH. HP-Lattice QSAR for dynein proteins: experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence. Bioorg Med Chem. 2008;16:7770–7776.
   PubMed Web of Science ®Google Scholar
• Prado-PradoFJ, Martinez de la VegaO, UriarteE, UbeiraFM, ChouKC, González-DíazH. Unified QSAR approach to antimicrobials. 4. Multi-target QSAR modeling and comparative multi-distance study of the giant components of antiviral drug–drug complex networks. Bioorg Med Chem. 2009;17:569–575.
   PubMed Web of Science ®Google Scholar
• Prado-PradoFJ, González-DíazH, de la VegaOM, UbeiraFM, ChouKC. Unified QSAR approach to antimicrobials. Part 3: first multi-tasking QSAR model for input-coded prediction, structural back-projection, and complex networks clustering of antiprotozoal compounds. Bioorg Med Chem. 2008;16:5871–5880.
   PubMed Web of Science ®Google Scholar
• DuQS, HuangRB, WeiYT, PangZW, DuLQ, ChouKC. Fragment-based quantitative structure–activity relationship (FB-QSAR) for fragment-based drug design. J Comput Chem. 2009;30:295–304.
   PubMed Web of Science ®Google Scholar
• HouX, DuJ, FangH, LiM. 3D-QSAR study on a series of Bcl-2 protein inhibitors using comparative molecular field analysis. Protein Pept Lett. 2011;18:440–449.
   PubMed Web of Science ®Google Scholar
• ChouKC. Structural bioinformatics and its impact to biomedical science. Curr Med Chem. 2004;11:2105–2134.
   PubMed Web of Science ®Google Scholar
• ChouKC. Molecular therapeutic target for type-2 diabetes. J Proteome Res. 2004;3:1284–1288.
   PubMed Web of Science ®Google Scholar
• SiroisS, WeiDQ, DuQ, ChouKC. Virtual screening for SARS-CoV protease based on KZ7088 pharmacophore points. J Chem Inf Comput Sci. 2004;44:1111–1122.
   PubMedGoogle Scholar
• MaY, WangSQ, XuWR, WangRL, ChouKC. Design novel dual agonists for treating type-2 diabetes by targeting peroxisome proliferator-activated receptors with core hopping approach. PLoS One. 2012;7:e38546.
   PubMed Web of Science ®Google Scholar
• LiXB, WangSQ, XuWR, WangRL, ChouKC. Novel inhibitor design for hemagglutinin against H1N1 influenza virus by core hopping method. PLoS One. 2011;6:e28111.
   PubMed Web of Science ®Google Scholar
• CombiGlide2.5. New York, NY: Schrodinger LLC; 2009.
   Google Scholar
• BermanHM, BattistuzT, BhatTN, BluhmWF, BournePE, BurkhardtK, FengZ, GillilandGL, IypeL, JainS, FaganP, MarvinJ, PadillaD, RavichandranV, SchneiderB, ThankiN, WeissigH, WestbrookJD, ZardeckiC. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 2002;58:899–907.
   PubMed Web of Science ®Google Scholar
• ZhangX, HeY, LiuS, YuZ, JiangZX, YangZ, DongY, NabingerSC, WuL, GunawanAM, WangL, ChanRJ, ZhangZY. Salicylic acid based small molecule inhibitor for the oncogenic Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2). J Med Chem. 2010;53:2482–2493.
   PubMed Web of Science ®Google Scholar
• FriesnerRA, BanksJL, MurphyRB, HalgrenTA, KlicicJJ, MainzDT, RepaskyMP, KnollEH, ShelleyM, PerryJK, ShawDE, FrancisP, ShenkinPS. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004;47:1739–1749.
   PubMed Web of Science ®Google Scholar
• Schrodinger-LLC. Schrodinger Suite 2009 Virtual Screening Workflow, Glide version 5.5. New York, NY: Schrodinger-LLC; 2009.
   Google Scholar
• IrwinJJ, ShoichetBK. ZINC – a free database of commercially available compounds for virtual screening. J Chem Inf Model. 2005;45:177–182.
   PubMed Web of Science ®Google Scholar
• ChouKC. Low-frequency collective motion in biomacromolecules and its biological functions. Biophys Chem. 1988;30:3–48.
   PubMed Web of Science ®Google Scholar
• ChouKC. The biological functions of low-frequency vibrations (phonons). 3. Resonance effects and allosteric transition. Biophys Chem. 1984;20:881–890.
   Google Scholar
• WangJF, ChouKC. Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations. Biochem Biophys Res Commun. 2009;390:608–612.
   PubMed Web of Science ®Google Scholar
• ChouKC. Low-frequency resonance and cooperativity of hemoglobin. Trends Biochem Sci. 1989;14:212–213.
   PubMed Web of Science ®Google Scholar
• ChouKC. The biological functions of low-frequency vibrations (phonons). 4. Resonance effects and allosteric transition. Biophys Chem. 1984;20:61–71.
   PubMed Web of Science ®Google Scholar
• ChouKC. The biological functions of low-frequency vibrations (phonons). VI. A possible dynamic mechanism of allosteric transition in antibody molecules. Biopolymers. 1987;26:285–295.
   PubMed Web of Science ®Google Scholar
• ChouKC, MaoB. Collective motion in DNA and its role in drug intercalation. Biopolymers. 1988;27:1795–1815.
   PubMed Web of Science ®Google Scholar
• ChouKC, ZhangCT, MaggioraGM. Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth. Biopolymers. 1994;34:143–153.
   PubMed Web of Science ®Google Scholar
• JorgensenWL, DuffyEM. Prediction of drug solubility from structure. Adv Drug Deliv Rev. 2002;54:355–366.
   PubMed Web of Science ®Google Scholar
• QikProp3.2. New York, NY: Schrodinger LLC; 2009.
   Google Scholar
• SinghKhD, KirubakaranP, NagarajanS, SakkiahS, MuthusamyK, VelmurganD, JeyakanthanJ. Homology modeling, molecular dynamics, e-pharmacophore mapping and docking study of Chikungunya virus nsP2 protease. J Mol Model. 2012;18:39–51.
   PubMed Web of Science ®Google Scholar
• LipinskiCA, LombardoF, DominyBW, FeeneyPJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 2001;46:3–26.
   PubMed Web of Science ®Google Scholar