Structural insights of cyclin dependent kinases: Implications in design of selective inhibitors
Tài liệu tham khảo
Hanahan, 2011, Hallmarks of cancer: the next generation, Cell, 144, 646, 10.1016/j.cell.2011.02.013
Hanahan, 2000, The hallmarks of cancer, Cell, 100, 57, 10.1016/S0092-8674(00)81683-9
Chauhan, 2016, Dual inhibitors of epidermal growth factor receptor and topoisomerase IIα derived from a quinoline scaffold, RSC Adv., 6, 77717, 10.1039/C6RA15118C
Joshi, 2015, Growth factors mediated cell signalling in prostate cancer progression: implications in discovery of anti-prostate cancer agents, Chem. Biol. Interact., 240, 120, 10.1016/j.cbi.2015.08.009
Malumbres, 2014, Cyclin-dependent kinases, Genome Biol., 15, 1, 10.1186/gb4184
Harper, 2001, Cyclin-dependent kinases, Chem. Rev., 101, 2511, 10.1021/cr0001030
Zhang, 2009, Targeting cancer with small molecule kinase inhibitors, Nat. Rev. Canc., 9, 28, 10.1038/nrc2559
Nigg, 1995, Cyclin-dependent protein kinases: key regulators of the eukaryotic cell cycle, Bioessays, 17, 471, 10.1002/bies.950170603
Matsushime, 1994, D-type cyclin-dependent kinase activity in mammalian cells, Mol. Cell. Biol., 14, 2066, 10.1128/MCB.14.3.2066
Giacinti, 2006, RB and cell cycle progression, Oncogene, 25, 5220, 10.1038/sj.onc.1209615
Chen, 2009, A conserved phosphorylation site within the forkhead domain of FoxM1B is required for its activation by cyclin-CDK1, J. Biol. Chem., 284, 30695, 10.1074/jbc.M109.007997
Russo, 1996, Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A-Cdk2 complex, Nature, 382, 325, 10.1038/382325a0
Tomashevski, 2010, Cyclin C-dependent cell cycle entry is required for activation of nonhomologous end joining DNA repair in postmitotic neurons, Cell Death Differ., 17, 1189, 10.1038/cdd.2009.221
Aggarwal, 2010, Nuclear cyclin D1/CDK4 kinase regulates CUL4 expression and triggers neoplastic growth via activation of the PRMT5 methyltransferase, Cancer Cell, 18, 329, 10.1016/j.ccr.2010.08.012
Lavoie, 2011, Phosphorylation of human DNMT1: implication of cyclin-dependent kinases, Biochem. Biophys. Res. Commun., 409, 187, 10.1016/j.bbrc.2011.04.115
Fisher, 1994, A novel cyclin associates with M015/CDK7 to form the CDK-activating kinase, Cell, 78, 713, 10.1016/0092-8674(94)90535-5
Firestein, 2008, CDK8 is a colorectal cancer oncogene that regulates β-catenin activity, Nature, 455, 547, 10.1038/nature07179
Dale, 2015, A selective chemical probe for exploring the role of CDK8 and CDK19 in human disease, Nat. Chem. Biol., 11, 973, 10.1038/nchembio.1952
David, 2010, Cyclin-dependent kinase 9–cyclin K functions in the replication stress response, EMBO Rep., 11, 876, 10.1038/embor.2010.153
Zhong, 2012, Clinical and biological significance of Cdk10 in hepatocellular carcinoma, Gene, 498, 68, 10.1016/j.gene.2012.01.022
Hu, 2003, CDK11 complexes promote pre-mRNA splicing, J. Biol. Chem., 278, 8623, 10.1074/jbc.M210057200
Blazek, 2011, The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes, Genes Dev., 25, 2158, 10.1101/gad.16962311
Cheng, 2012, Interaction of cyclin-dependent kinase 12/CrkRS with cyclin K1 is required for the phosphorylation of the C-terminal domain of RNA polymerase II, Mol. Cell. Biol., 32, 4691, 10.1128/MCB.06267-11
Davidson, 2010, The Cell Cycle and Wnt, 1667
Park, 2014, ALS2CR7 (CDK15) attenuates TRAIL induced apoptosis by inducing phosphorylation of survivin Thr34, Biochem. Biophys. Res. Commun., 450, 129, 10.1016/j.bbrc.2014.05.070
Mikolcevic, 2012, Cyclin-dependent kinase 16/PCTAIRE kinase 1 is activated by cyclin Y and is essential for spermatogenesis, Mol. Cell. Biol., 32, 868, 10.1128/MCB.06261-11
Tan, 2009, Sp1 phosphorylation and its regulation of gene transcription, Mol. Cell. Biol., 29, 2483, 10.1128/MCB.01828-08
Matsuda, 2017, PCTK3/CDK18 regulates cell migration and adhesion by negatively modulating FAK activity, Sci. Rep., 7, 45545, 10.1038/srep45545
Liu, 2004, p42, a novel cyclin-dependent kinase-activating kinase in mammalian cells, J. Biol. Chem., 279, 4507, 10.1074/jbc.M309995200
Taylor, 2009, 429
Ford, 1998, The S phase: beginning, middle, and end: a perspective, J. Cell. Biochem., 72, 1, 10.1002/(SICI)1097-4644(1998)72:30/31+<1::AID-JCB2>3.0.CO;2-E
Lundberg, 1998, Functional inactivation of the retinoblastoma protein requires sequential modification by at least two distinct cyclin-cdk complexes, Mol. Cell. Biol., 18, 753, 10.1128/MCB.18.2.753
Sherr, 2000, The Pezcoller lecture: cancer cell cycles revisited, Cancer Res., 60, 3689
Mourón, 2010, C is required to sustain the spindle-assembly checkpoint, J. Cell Sci., 123, 2586, 10.1242/jcs.059964
Nebreda, 2006, CDK activation by non-cyclin proteins, Curr. Opin. Cell Biol., 18, 192, 10.1016/j.ceb.2006.01.001
Marais, 2010, Cell cycle-dependent regulation of the forkhead transcription factor FOXK2 by CDK· cyclin complexes, J. Biol. Chem., 285, 35728, 10.1074/jbc.M110.154005
Zhao, 2012, Regulation of lipogenesis by cyclin-dependent kinase 8–mediated control of SREBP-1, J. Clin. Invest., 122, 2417, 10.1172/JCI61462
Bienvenu, 2010, Transcriptional role of cyclin D1 in development revealed by a genetic–proteomic screen, Nature, 463, 374, 10.1038/nature08684
Odajima, 2011, Cyclin E constrains Cdk5 activity to regulate synaptic plasticity and memory formation, Dev. Cell, 21, 655, 10.1016/j.devcel.2011.08.009
Bartkowiak, 2010, CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1, Genes Dev., 24, 2303, 10.1101/gad.1968210
Lim, 2013, Cdks, cyclins and CKIs: roles beyond cell cycle regulation, Development, 140, 3079, 10.1242/dev.091744
Davidson, 2009, Cell cycle control of wnt receptor activation, Dev. Cell, 17, 788, 10.1016/j.devcel.2009.11.006
Morgan, 2007
Ortega, 2002, Cyclin D-dependent kinases, INK4 inhibitors and cancer, BBA Rev. Cancer, 1602, 73
Cánepa, 2007, INK4 proteins, a family of mammalian CDK inhibitors with novel biological functions, IUBMB life, 59, 419, 10.1080/15216540701488358
Roussel, 1999, The INK4 family of cell cycle inhibitors in cancer, Oncogene, 18, 5311, 10.1038/sj.onc.1202998
Wang, 2003, Cdk5 activation induces hippocampal CA1 cell death by directly phosphorylating NMDA receptors, Nat. Neurosci., 6, 1039, 10.1038/nn1119
Schang, 2004, Effects of pharmacological cyclin-dependent kinase inhibitors on viral transcription and replication, Biochim. Biophys. Acta-Proteins Proteom., 1697, 197, 10.1016/j.bbapap.2003.11.024
Tsai, 2004, Cdk5, a therapeutic target for Alzheimer's disease?, Biochim. Biophys. Acta-Proteins Proteom., 1697, 137, 10.1016/j.bbapap.2003.11.019
Smith, 2004, CDKs: taking on a role as mediators of dopaminergic loss in Parkinson's disease, Trends Mol. Med., 10, 445, 10.1016/j.molmed.2004.07.003
Smith, 2003, Cyclin-dependent kinase 5 is a mediator of dopaminergic neuron loss in a mouse model of Parkinson's disease, Proc. Natl. Acad. Sci., 100, 13650, 10.1073/pnas.2232515100
Nelson, 2005, Therapeutics in renal disease: the road ahead for antiproliferative targets, Nephron Exp. Nephrol., 103, e6, 10.1159/000090138
L. Meijer, Pharmacological Inhibitors of Disease-relevant Cyclin-dependent Kinases.
Roskoski, 2015, A historical overview of protein kinases and their targeted small molecule inhibitors, Pharmacol. Res., 100, 1, 10.1016/j.phrs.2015.07.010
Li, 2016, Recent progress of cyclin-dependent kinase inhibitors as potential anticancer agents, Future Med. Chem., 8, 2047, 10.4155/fmc-2016-0129
Betzi, 2011, Discovery of a potential allosteric ligand binding site in CDK2, ACS Chem. Biol., 6, 492, 10.1021/cb100410m
Rastelli, 2014, Structure-based discovery of the first allosteric inhibitors of cyclin-dependent kinase 2, Cell Cycle, 13, 2296, 10.4161/cc.29295
Asghar, 2015, The history and future of targeting cyclin-dependent kinases in cancer therapy, Nat. Rev. Drug Discov., 14, 130, 10.1038/nrd4504
Besson, 2008, CDK inhibitors: cell cycle regulators and beyond, Dev. Cell, 14, 159, 10.1016/j.devcel.2008.01.013
Sánchez-Martínez, 2015, Cyclin dependent kinase (CDK) inhibitors as anticancer drugs, Bioorg. Med. Chem. Lett., 25, 3420, 10.1016/j.bmcl.2015.05.100
Li, 2016, Recent progress of cyclin-dependent kinase inhibitors as potential anticancer agents, Future, 8, 2047
Brown, 2015, CDK1 structures reveal conserved and unique features of the essential cell cycle CDK, Nat. Comm., 6, 6769, 10.1038/ncomms7769
Jacobsen, 2012, Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase, J. Am. Chem. Soc., 134, 15357, 10.1021/ja304419t
Ayaz, 2016, Conformational adaption may explain the slow dissociation kinetics of roniciclib (BAY 1000394), a type I CDK inhibitor with kinetic selectivity for CDK2 and CDK9, ACS Chem. Biol., 11, 1710, 10.1021/acschembio.6b00074
Blake, 2016, Discovery of (S)-1-(1-(4-Chloro-3-fluorophenyl)-2-hydroxyethyl)-4-(2-((1-methyl-1H-pyrazol-5-yl) amino) pyrimidin-4-yl) pyridin-2 (1H)-one (GDC-0994), an extracellular signal-regulated kinase 1/2 (ERK1/2) inhibitor in early clinical development, J. Med. Chem., 59, 5650, 10.1021/acs.jmedchem.6b00389
Day, 2009, Crystal structure of human CDK4 in complex with a D-type cyclin, Proc. Natl. Acad. Sci., 106, 4166, 10.1073/pnas.0809645106
Takaki, 2009, The structure of CDK4/cyclin D3 has implications for models of CDK activation, Proc. Natl. Acad. Sci., 106, 4171, 10.1073/pnas.0809674106
Tarricone, 2001, Structure and regulation of the CDK5-p25 nck5a complex, Mol. Cell, 8, 657, 10.1016/S1097-2765(01)00343-4
Mapelli, 2005, Mechanism of CDK5/p25 binding by CDK inhibitors, J. Med. Chem., 48, 671, 10.1021/jm049323m
Ahn, 2005, Defining Cdk5 ligand chemical space with small molecule inhibitors of tau phosphorylation, Chem. Biol., 12, 811, 10.1016/j.chembiol.2005.05.011
Malmström, 2012, Synthesis and structure-activity relationship of 4-(1, 3-benzothiazol-2-yl)-thiophene-2-sulfonamides as cyclin-dependent kinase 5 (cdk5)/p25 inhibitors, Bioorg. Med. Chem. Lett., 22, 5919, 10.1016/j.bmcl.2012.07.068
Lu, 2005, Crystal structure of a human cyclin-dependent kinase 6 complex with a flavonol inhibitor, fisetin, J. Med. Chem., 48, 737, 10.1021/jm049353p
Lu, 2006, Toward understanding the structural basis of cyclin-dependent kinase 6 specific inhibition, J. Med. Chem., 49, 3826, 10.1021/jm0600388
Lolli, 2004, The crystal structure of human CDK7 and its protein recognition properties, Structure, 12, 2067, 10.1016/j.str.2004.08.013
Pelish, 2015, Mediator kinase inhibition further activates super-enhancer-associated genes in AML, Nature, 526, 273, 10.1038/nature14904
Schneider, 2013, Structure–kinetic relationship study of CDK8/CycC specific compounds, Proc. Natl. Acad. Sci., 110, 8081, 10.1073/pnas.1305378110
Baumli, 2012, The CDK9 C-helix exhibits conformational plasticity that may explain the selectivity of CAN508, ACS Chem. Biol., 7, 811, 10.1021/cb2004516
Baumli, 2010, Halogen bonds form the basis for selective P-TEFb inhibition by DRB, Chem. Biol., 17, 931, 10.1016/j.chembiol.2010.07.012
Baumli, 2008, the structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation, EMBO J., 27, 1907, 10.1038/emboj.2008.121
Bettayeb, 2010, CDK inhibitors roscovitine and CR8 trigger Mcl-1 down-regulation and apoptotic cell death in neuroblastoma cells, Genes Cancer, 1, 369, 10.1177/1947601910369817
Dixon-Clarke, 2015, Structures of the CDK12/CycK complex with AMP-PNP reveal a flexible C-terminal kinase extension important for ATP binding, Sci. Rep., 5, 17122, 10.1038/srep17122
Bösken, 2014, The structure and substrate specificity of human Cdk12/Cyclin K, Nat. Comm., 5, 3505, 10.1038/ncomms4505
Greifenberg, 2016, Analysis of the cdk13/cyclin K complex, Cell Rep., 14, 320, 10.1016/j.celrep.2015.12.025
Castedo, 2004, Cell death by mitotic catastrophe: a molecular definition, Oncogene, 23, 2825, 10.1038/sj.onc.1207528
P. Schrödinger, version 3.5, LLC, New York, NY, (2014).
Jacobson, 2004, A hierarchical approach to all-atom protein loop prediction, Proteins Struct. Funct. Bioinf., 55, 351, 10.1002/prot.10613
Jacobson, 2002, On the role of the crystal environment in determining protein side-chain conformations, J. Mol. Biol., 320, 597, 10.1016/S0022-2836(02)00470-9
Parry, 2010, Dinaciclib (SCH 727965), a novel and potent cyclin-dependent kinase inhibitor, Mol. Cancer Ther., 9, 2344, 10.1158/1535-7163.MCT-10-0324
Kwiatkowski, 2014, Targeting transcription regulation in cancer with a covalent CDK7 inhibitor, Nature, 511, 616, 10.1038/nature13393
Zhao, 2017, Determining cysteines available for covalent inhibition across the human kinome, J. Med. Chem., 60, 2879, 10.1021/acs.jmedchem.6b01815
Zhang, 2016, Covalent targeting of remote cysteine residues to develop CDK12 and 13 inhibitors, Nat. Chem. Biol., 12, 876, 10.1038/nchembio.2166
Mascarenhas, 2008, Combined ligand and structure based approaches for narrowing on the essential physicochemical characteristics for CDK4 inhibition, J, Chem. Inf. Model., 48, 1325, 10.1021/ci8000343
Shafiq, 2012, Fascaplysin as a specific inhibitor for CDK4: insights from molecular modelling, PLoS One, 7, e42612, 10.1371/journal.pone.0042612
Broto, 1984, Molecular structures: perception, autocorrelation descriptor and SAR studies. Autocorrelation descriptor, Eur. J. Med. Chem., 19, 66
Gasteiger, 1996, Chemical information in 3D space, J. Chem. Inf. Comp. Sci., 36, 1030, 10.1021/ci960343+
Todeschini, 1997, 3D-modelling and prediction by WHIM descriptors. 6. Application of WHIM descriptors in QSAR studies, Quant. Struct.-Act. Relat., 16, 120, 10.1002/qsar.19970160204
González, 2005, GETAWAY descriptors to predicting A 2A adenosine receptors agonists, Eur. J. Med. Chem., 40, 1080, 10.1016/j.ejmech.2005.04.014
Yap, 2011, PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints, J. Comput. Chem., 32, 1466, 10.1002/jcc.21707
Kalra, 2013, Modeling of antitubercular activity of biphenyl analogs of 2-nitroimidazo [2, 1-b][1, 3] oxazine to rationalize their activity profile, Med. Chem. Res., 22, 3444, 10.1007/s00044-012-0348-8