Developing Irreversible Inhibitors of the Protein Kinase Cysteinome

Bansal, 2003, Specific inhibitor of FGF receptor signaling: FGF-2-mediated effects on proliferation, differentiation, and MAPK activation are inhibited by PD173074 in oligodendrocyte-lineage cells, J. Neurosci. Res., 74, 486, 10.1002/jnr.10773 Barf, 2012, Irreversible protein kinase inhibitors: balancing the benefits and risks, J. Med. Chem., 55, 6243, 10.1021/jm3003203 Barluenga, 2010, In vivo efficacy of natural product-inspired irreversible kinase inhibitors, ChemBioChem, 11, 1692, 10.1002/cbic.201000205 Bernier, 2006, Binding of manumycin A inhibits IkappaB kinase beta activity, J. Biol. Chem., 281, 2551, 10.1074/jbc.M511878200 Caffrey, 2007, PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments, BMC Bioinformatics, 8, 381, 10.1186/1471-2105-8-381 Chalker, 2009, Chemical modification of proteins at cysteine: opportunities in chemistry and biology, Chem. Asian J., 4, 630, 10.1002/asia.200800427 Changeux, 2011, Conformational selection or induced fit? 50 years of debate resolved, F1000 Biol. Rep., 3, 19, 10.3410/B3-19 Cohen, 2005, Structural bioinformatics-based design of selective, irreversible kinase inhibitors, Science, 308, 1318, 10.1126/science1108367 Cohen, 2002, The origins of protein phosphorylation, Nat. Cell Biol., 4, E127, 10.1038/ncb0502-e127 Cowan-Jacob, 2007, Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia, Acta Crystallogr. D Biol. Crystallogr., 63, 80, 10.1107/S0907444906047287 Davis, 2011, Comprehensive analysis of kinase inhibitor selectivity, Nat. Biotechnol., 29, 1046, 10.1038/nbt.1990 Engelman, 2007, PF00299804, an irreversible pan-ERBB inhibitor, is effective in lung cancer models with EGFR and ERBB2 mutations that are resistant to gefitinib, Cancer Res., 67, 11924, 10.1158/0008-5472.CAN-07-1885 Fabian, 2005, A small molecule-kinase interaction map for clinical kinase inhibitors, Nat. Biotechnol., 23, 329, 10.1038/nbt1068 Fry, 1998, Specific, irreversible inactivation of the epidermal growth factor receptor and erbB2, by a new class of tyrosine kinase inhibitor, Proc. Natl. Acad. Sci. USA, 95, 12022, 10.1073/pnas.95.20.12022 Garuti, 2011, Irreversible protein kinase inhibitors, Curr. Med. Chem., 18, 2981, 10.2174/092986711796391705 Goto, 2009, J. Pharmacol. Exp. Ther., 331, 485, 10.1124/jpet.109.156554 Haber, 2011, The evolving war on cancer, Cell, 145, 19, 10.1016/j.cell.2011.03.026 Hanahan, 2011, Hallmarks of cancer: the next generation, Cell, 144, 646, 10.1016/j.cell.2011.02.013 Henise, 2011, Irreversible Nek2 kinase inhibitors with cellular activity, J. Med. Chem., 54, 4133, 10.1021/jm200222m Hernandes, 2010, Halogen atoms in the modern medicinal chemistry: hints for the drug design, Curr. Drug Targets, 11, 303, 10.2174/138945010790711996 Honigberg, 2010, The Bruton tyrosine kinase inhibitor PCI-32765 blocks B-cell activation and is efficacious in models of autoimmune disease and B-cell malignancy, Proc. Natl. Acad. Sci. USA, 107, 13075, 10.1073/pnas.1004594107 Hunter, 1980, Transforming gene product of Rous sarcoma virus phosphorylates tyrosine, Proc. Natl. Acad. Sci. USA, 77, 1311, 10.1073/pnas.77.3.1311 Hur, 2008, Clinical stage EGFR inhibitors irreversibly alkylate Bmx kinase, Bioorg. Med. Chem. Lett., 18, 5916, 10.1016/j.bmcl.2008.07.062 Jacob, 2012, Control of oxidative posttranslational cysteine modifications: from intricate chemistry to widespread biological and medical applications, Chem. Res. Toxicol., 25, 588, 10.1021/tx200342b Jogireddy, 2009, Synthesis of a resorcylic acid lactone (RAL) library using fluorous-mixture synthesis and profile of its selectivity against a panel of kinases, Chemistry, 15, 11498, 10.1002/chem.200901375 Johnson, 2010, Strategies for discovering and derisking covalent, irreversible enzyme inhibitors, Future Med. Chem., 2, 949, 10.4155/fmc.10.21 Karaman, 2008, A quantitative analysis of kinase inhibitor selectivity, Nat. Biotechnol., 26, 127, 10.1038/nbt1358 Kontzias, 2012, Kinase inhibitors in the treatment of immune-mediated disease, F1000. Med-Rep., 4, 5, 10.3410/M4-5 Kwok, 2001, The anti-inflammatory natural product parthenolide from the medicinal herb Feverfew directly binds to and inhibits IkappaB kinase, Chem. Biol., 8, 759, 10.1016/S1074-5521(01)00049-7 Lebakken, 2009, Development and applications of a broad-coverage, TR-FRET-based kinase binding assay platform, J. Biomol. Screen., 14, 924, 10.1177/1087057109339207 Lee, 2006, Inhibition of NF-kappa B activation through targeting I kappa B kinase by celastrol, a quinone methide triterpenoid, Biochem. Pharmacol., 72, 1311, 10.1016/j.bcp.2006.08.014 Leonard, 2011, Redox-based probes for protein tyrosine phosphatases, Angew. Chem. Int. Ed. Engl., 50, 4423, 10.1002/anie.201007871 Leproult, 2011, Cysteine mapping in conformationally distinct kinase nucleotide binding sites: application to the design of selective covalent inhibitors, J. Med. Chem., 54, 1347, 10.1021/jm101396q Li, 2008, BIBW2992, an irreversible EGFR/HER2 inhibitor highly effective in preclinical lung cancer models, Oncogene, 27, 4702, 10.1038/onc.2008.109 Liu, 2006, Rational design of inhibitors that bind to inactive kinase conformations, Nat. Chem. Biol., 2, 358, 10.1038/nchembio799 Liu, 2012, Natural products as kinase inhibitors, Nat. Prod. Rep., 29, 392, 10.1039/c2np00097k Liu, 2012, Kinome-wide selectivity profiling of ATP-competitive mammalian target of rapamycin (mTOR) inhibitors and characterization of their binding kinetics, J. Biol. Chem., 287, 9742, 10.1074/jbc.M111.304485 Manning, 2002, Evolution of protein kinase signaling from yeast to man, Trends Biochem. Sci., 27, 514, 10.1016/S0968-0004(02)02179-5 Manning, 2002, The protein kinase complement of the human genome, Science, 298, 1912, 10.1126/science.1075762 Muramoto, 2010, J. Pharmacol. Exp. Ther., 335, 23, 10.1124/jpet.110.168583 Nakayama, 2009, A zone classification system for risk assessment of idiosyncratic drug toxicity using daily dose and covalent binding, Drug Metab. Dispos., 37, 1970, 10.1124/dmd.109.027797 Ohori, 2007, Role of a cysteine residue in the active site of ERK and the MAPKK family, Biochem. Biophys. Res. Commun., 353, 633, 10.1016/j.bbrc.2006.12.083 Okerberg, 2005, High-resolution functional proteomics by active-site peptide profiling, Proc. Natl. Acad. Sci. USA, 102, 4996, 10.1073/pnas.0501205102 Patricelli, 2007, Functional interrogation of the kinome using nucleotide acyl phosphates, Biochemistry, 46, 350, 10.1021/bi062142x Patricelli, 2011, In situ kinase profiling reveals functionally relevant properties of native kinases, Chem. Biol., 18, 699, 10.1016/j.chembiol.2011.04.011 Perez, 2009, Thienylhalomethylketones: Irreversible glycogen synthase kinase 3 inhibitors as useful pharmacological tools, Bioorg. Med. Chem., 17, 6914, 10.1016/j.bmc.2009.08.042 Potashman, 2009, Covalent modifiers: an orthogonal approach to drug design, J. Med. Chem., 52, 1231, 10.1021/jm8008597 Rosell, 2009, Screening for epidermal growth factor receptor mutations in lung cancer, N. Engl. J. Med., 361, 958, 10.1056/NEJMoa0904554 Rossi, 2000, Anti-inflammatory cyclopentenone prostaglandins are direct inhibitors of IkappaB kinase, Nature, 403, 103, 10.1038/47520 Rusnak, 2001, The effects of the novel, reversible epidermal growth factor receptor/ErbB-2 tyrosine kinase inhibitor, GW2016, on the growth of human normal and tumor-derived cell lines in vitro and in vivo, Mol. Cancer Ther., 1, 85 Schirmer, 2006, Targeted covalent inactivation of protein kinases by resorcylic acid lactone polyketides, Proc. Natl. Acad. Sci. USA, 103, 4234, 10.1073/pnas.0600445103 Serafimova, 2012, Reversible targeting of noncatalytic cysteines with chemically tuned electrophiles, Nat. Chem. Biol., 8, 471, 10.1038/nchembio.925 Singh, 1997, Structure-based design of a potent, selective, and irreversible inhibitor of the catalytic domain of the erbB receptor subfamily of protein tyrosine kinases, J. Med. Chem., 40, 1130, 10.1021/jm960380s Singh, 2010, Targeted covalent drugs of the kinase family, Curr. Opin. Chem. Biol., 14, 475, 10.1016/j.cbpa.2010.06.168 Singh, 2011, The resurgence of covalent drugs, Nat. Rev. Drug Discov., 10, 307, 10.1038/nrd3410 Smaill, 2000, Tyrosine kinase inhibitors. 17. Irreversible inhibitors of the epidermal growth factor receptor: 4-(phenylamino)quinazoline- and 4-(phenylamino)pyrido[3,2-d]pyrimidine-6-acrylamides bearing additional solubilizing functions, J. Med. Chem., 43, 1380, 10.1021/jm990482t Smith, 2009, Beyond picomolar affinities: quantitative aspects of noncovalent and covalent binding of drugs to proteins, J. Med. Chem., 52, 225, 10.1021/jm800498e Sonoda, 1999, Suppression of oncogenic transformation by hypothemycin associated with accelerated cyclin D1 degradation through ubiquitin-proteasome pathway, Life Sci., 65, 381, 10.1016/S0024-3205(99)00259-3 Thompson, 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673 Tsou, 2005, Optimization of 6,7-disubstituted-4-(arylamino)quinoline-3-carbonitriles as orally active, irreversible inhibitors of human epidermal growth factor receptor-2 kinase activity, J. Med. Chem., 48, 1107, 10.1021/jm040159c Uetrecht, 2008, Idiosyncratic drug reactions: past, present, and future, Chem. Res. Toxicol., 21, 84, 10.1021/tx700186p Underwood, 2000, SB 239063, a potent p38 MAP kinase inhibitor, reduces inflammatory cytokine production, airways eosinophil infiltration, and persistence, J. Pharmacol. Exp. Ther., 293, 281 Winssinger, 2007, Chemistry and biology of resorcylic acid lactones, Chem. Commun. (Camb.), 22, 10.1039/B610344H Wissner, 2008, The development of HKI-272 and related compounds for the treatment of cancer, Arch. Pharm. (Weinheim), 341, 465, 10.1002/ardp.200800009 Wissner, 2005, 2-(Quinazolin-4-ylamino)-[1,4]benzoquinones as covalent-binding, irreversible inhibitors of the kinase domain of vascular endothelial growth factor receptor-2, J. Med. Chem., 48, 7560, 10.1021/jm050559f Wissner, 2007, Dual irreversible kinase inhibitors: quinazoline-based inhibitors incorporating two independent reactive centers with each targeting different cysteine residues in the kinase domains of EGFR and VEGFR-2, Bioorg. Med. Chem., 15, 3635, 10.1016/j.bmc.2007.03.055 Yan, 2008, 17-Acetoxyjolkinolide B irreversibly inhibits IkappaB kinase and induces apoptosis of tumor cells, Mol. Cancer Ther., 7, 1523, 10.1158/1535-7163.MCT-08-0263 Yoshimura, 2006, EKB-569, a new irreversible epidermal growth factor receptor tyrosine kinase inhibitor, with clinical activity in patients with non-small cell lung cancer with acquired resistance to gefitinib, Lung Cancer, 51, 363, 10.1016/j.lungcan.2005.10.006 Yun, 2007, Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity, Cancer Cell, 11, 217, 10.1016/j.ccr.2006.12.017 Zapf, 2012, Covalent inhibitors of interleukin-2 inducible T cell kinase (itk) with nanomolar potency in a whole-blood assay, J. Med. Chem., 55, 10047, 10.1021/jm301190s Zhang, 2009, Targeting cancer with small molecule kinase inhibitors, Nat. Rev. Cancer, 9, 28, 10.1038/nrc2559 Zhang, 2012, Discovery of potent and selective covalent inhibitors of JNK, Chem. Biol., 19, 140, 10.1016/j.chembiol.2011.11.010 Zhou, 2009, Novel mutant-selective EGFR kinase inhibitors against EGFR T790M, Nature, 462, 1070, 10.1038/nature08622 Zhou, 2010, A structure-guided approach to creating covalent FGFR inhibitors, Chem. Biol., 17, 285, 10.1016/j.chembiol.2010.02.007