The Landscape of Atypical and Eukaryotic Protein Kinases.

Published in: Trends in Pharmacological Sciences DOI: 10.1016/j.tips.2019.09.002 Publication date: 2019 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Kanev, G. K., de Graaf, C., de Esch, I. J. P., Leurs, R., Würdinger, T., Westerman, B. A., & Kooistra, A. J. (2019). The Landscape of Atypical and Eukaryotic Protein Kinases. Trends in Pharmacological Sciences, 40(11), 818-832. https://doi.org/10.1016/j.tips.2019.09.002

[1]  Susan S. Taylor,et al.  Evolution of a dynamic molecular switch , 2019, IUBMB life.

[2]  Steven J. M. Jones,et al.  Oncogenic Signaling Pathways in The Cancer Genome Atlas. , 2018, Cell.

[3]  Stéphane Bourg,et al.  PKIDB: A Curated, Annotated and Updated Database of Protein Kinase Inhibitors in Clinical Trials , 2018, Molecules.

[4]  James Scott-Brown,et al.  Visualization and analysis of non-covalent contacts using the Protein Contacts Atlas , 2018, Nature structural & molecular biology.

[5]  P. Poulikakos,et al.  New perspectives for targeting RAF kinase in human cancer , 2017, Nature Reviews Cancer.

[6]  Lewis C. Cantley,et al.  The PI3K Pathway in Human Disease , 2017, Cell.

[7]  David R. Spring,et al.  A fragment-based approach leading to the discovery of a novel binding site and the selective CK2 inhibitor CAM4066 , 2017, Bioorganic & medicinal chemistry.

[8]  S. Knapp,et al.  Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer , 2017, Nature Communications.

[9]  T. Kinoshita,et al.  The juxtamembrane region of TrkA kinase is critical for inhibitor selectivity. , 2017, Bioorganic & medicinal chemistry letters.

[10]  Bert Vogelstein,et al.  Identification of allosteric binding sites for PI3Kα oncogenic mutant specific inhibitor design. , 2017, Bioorganic & medicinal chemistry.

[11]  P. Aloy,et al.  Quantification of Pathway Cross-talk Reveals Novel Synergistic Drug Combinations for Breast Cancer. , 2017, Cancer research.

[12]  Stephen J. Capuzzi,et al.  Development of Narrow Spectrum ATP-competitive Kinase Inhibitors as Probes for BIKE and AAK1 , 2016, bioRxiv.

[13]  Mingming Jia,et al.  COSMIC: somatic cancer genetics at high-resolution , 2016, Nucleic Acids Res..

[14]  M. Clausen,et al.  Allosteric small-molecule kinase inhibitors. , 2015, Pharmacology & therapeutics.

[15]  Chris de Graaf,et al.  KLIFS: a structural kinase-ligand interaction database , 2015, Nucleic Acids Res..

[16]  R. Roskoski A historical overview of protein kinases and their targeted small molecule inhibitors. , 2015, Pharmacological research.

[17]  D. Fabbro,et al.  Optimization of a Dibenzodiazepine Hit to a Potent and Selective Allosteric PAK1 Inhibitor. , 2015, ACS medicinal chemistry letters.

[18]  F. Maltais,et al.  Structural basis for isoform selectivity in a class of benzothiazole inhibitors of phosphoinositide 3-kinase γ. , 2015, Journal of medicinal chemistry.

[19]  Jean J. Zhao,et al.  PI3K in cancer: divergent roles of isoforms, modes of activation and therapeutic targeting , 2014, Nature Reviews Cancer.

[20]  Roger L. Williams,et al.  The structural basis for mTOR function. , 2014, Seminars in cell & developmental biology.

[21]  R. Wrobel,et al.  Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis. , 2014, Molecular cell.

[22]  Susan S. Taylor,et al.  Kinase Regulation by Hydrophobic Spine Assembly in Cancer , 2014, Molecular and Cellular Biology.

[23]  M. Bentires-Alj,et al.  Mechanism-based cancer therapy: resistance to therapy, therapy for resistance , 2014, Oncogene.

[24]  D. Erdmann,et al.  Characterization of the Novel and Specific PI3Kα Inhibitor NVP-BYL719 and Development of the Patient Stratification Strategy for Clinical Trials , 2014, Molecular Cancer Therapeutics.

[25]  S. Knapp,et al.  The structural basis of PI3K cancer mutations: from mechanism to therapy. , 2014, Cancer research.

[26]  I. D. de Esch,et al.  KLIFS: a knowledge-based structural database to navigate kinase-ligand interaction space. , 2014, Journal of medicinal chemistry.

[27]  Jean-Pierre Marquette,et al.  Discovery and optimization of pyrimidone indoline amide PI3Kβ inhibitors for the treatment of phosphatase and tensin homologue (PTEN)-deficient cancers. , 2014, Journal of medicinal chemistry.

[28]  P. Johnston,et al.  Cancer drug resistance: an evolving paradigm , 2013, Nature Reviews Cancer.

[29]  Doriano Fabbro,et al.  Discovery of NVP-BYL719 a potent and selective phosphatidylinositol-3 kinase alpha inhibitor selected for clinical evaluation. , 2013, Bioorganic & medicinal chemistry letters.

[30]  N. Pavletich,et al.  mTOR kinase structure, mechanism and regulation by the rapamycin-binding domain , 2013, Nature.

[31]  Benjamin E. Gross,et al.  Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal , 2013, Science Signaling.

[32]  Susan S. Taylor,et al.  Evolution of the eukaryotic protein kinases as dynamic molecular switches , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

[33]  L. Johnson,et al.  The structural basis for control of eukaryotic protein kinases. , 2012, Annual review of biochemistry.

[34]  Roger L. Williams,et al.  Regulation of lipid binding underlies the activation mechanism of class IA PI3-kinases , 2011, Oncogene.

[35]  John E. Burke,et al.  Structural Basis for Activation and Inhibition of Class I Phosphoinositide 3-Kinases , 2011, Science Signaling.

[36]  A. Hauschild,et al.  Improved survival with vemurafenib in melanoma with BRAF V600E mutation. , 2011, The New England journal of medicine.

[37]  J. Blenis,et al.  The Ras-ERK and PI3K-mTOR pathways: cross-talk and compensation. , 2011, Trends in biochemical sciences.

[38]  S. Digumarthy,et al.  Genotypic and Histological Evolution of Lung Cancers Acquiring Resistance to EGFR Inhibitors , 2011, Science Translational Medicine.

[39]  Susan S. Taylor,et al.  Protein kinases: evolution of dynamic regulatory proteins. , 2011, Trends in biochemical sciences.

[40]  R. Hruban,et al.  Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM) , 2010, Cancer biology & therapy.

[41]  J. Aten,et al.  In silico analysis of kinase expression identifies WEE1 as a gatekeeper against mitotic catastrophe in glioblastoma. , 2010, Cancer cell.

[42]  K. Shokat,et al.  Shaping Development of Autophagy Inhibitors with the Structure of the Lipid Kinase Vps34 , 2010, Science.

[43]  R. Morphy Selectively nonselective kinase inhibition: striking the right balance. , 2010, Journal of medicinal chemistry.

[44]  K. Shokat,et al.  Targeting the cancer kinome through polypharmacology , 2010, Nature Reviews Cancer.

[45]  A. Gazdar,et al.  Activating and resistance mutations of EGFR in non-small-cell lung cancer: role in clinical response to EGFR tyrosine kinase inhibitors , 2009, Oncogene.

[46]  R. Abraham,et al.  ATP-competitive inhibitors of the mammalian target of rapamycin: design and synthesis of highly potent and selective pyrazolopyrimidines. , 2009, Journal of medicinal chemistry.

[47]  Ralph Weissleder,et al.  Effective Use of PI3K and MEK Inhibitors to Treat Mutant K-Ras G12D and PIK3CA H1047R Murine Lung Cancers , 2008, Nature Medicine.

[48]  Lynn F. Ten Eyck,et al.  A helix scaffold for the assembly of active protein kinases , 2008, Proceedings of the National Academy of Sciences.

[49]  K. Kinzler,et al.  Dissecting isoform selectivity of PI3K inhibitors: the role of non-conserved residues in the catalytic pocket. , 2008, The Biochemical journal.

[50]  M. Meyerson,et al.  The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP , 2008, Proceedings of the National Academy of Sciences.

[51]  J. LoPiccolo,et al.  Targeting the PI3K/Akt/mTOR pathway: effective combinations and clinical considerations. , 2008, Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy.

[52]  E. Birney,et al.  Patterns of somatic mutation in human cancer genomes , 2007, Nature.

[53]  Susan S. Taylor,et al.  Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism , 2006, Proceedings of the National Academy of Sciences.

[54]  Richard Lugg,et al.  Mutation analysis of 24 known cancer genes in the NCI-60 cell line set , 2006, Molecular Cancer Therapeutics.

[55]  Philip E. Bourne,et al.  Structural Evolution of the Protein Kinase–Like Superfamily , 2005, PLoS Comput. Biol..

[56]  A. F. Neuwald,et al.  Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component? , 2005, Journal of molecular biology.

[57]  H. Lane,et al.  ERBB Receptors and Cancer: The Complexity of Targeted Inhibitors , 2005, Nature Reviews Cancer.

[58]  P. Vogt,et al.  Phosphatidylinositol 3-kinase mutations identified in human cancer are oncogenic. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[59]  N Srinivasan,et al.  Structural modes of stabilization of permissive phosphorylation sites in protein kinases: distinct strategies in Ser/Thr and Tyr kinases. , 2004, Journal of molecular biology.

[60]  J. Ptak,et al.  High Frequency of Mutations of the PIK3CA Gene in Human Cancers , 2004, Science.

[61]  P. Stahl,et al.  Lipid kinases play crucial and multiple roles in membrane trafficking and signaling. , 2003, Histology and histopathology.

[62]  J. Adams Activation loop phosphorylation and catalysis in protein kinases: is there functional evidence for the autoinhibitor model? , 2003, Biochemistry.

[63]  T. Hunter,et al.  The Protein Kinase Complement of the Human Genome , 2002, Science.

[64]  R. Pazdur,et al.  Approval summary: imatinib mesylate in the treatment of metastatic and/or unresectable malignant gastrointestinal stromal tumors. , 2002, Clinical cancer research : an official journal of the American Association for Cancer Research.

[65]  A. Nicholson,et al.  Mutations of the BRAF gene in human cancer , 2002, Nature.

[66]  P. Cohen,et al.  The origins of protein phosphorylation , 2002, Nature Cell Biology.

[67]  J Kuriyan,et al.  Crystal structure of the atypical protein kinase domain of a TRP channel with phosphotransferase activity. , 2001, Molecular cell.

[68]  John Kuriyan,et al.  Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571). , 2001, Cancer research.

[69]  P. Seeburg,et al.  Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. , 2000, Science.

[70]  Christian Ried,et al.  Structural insights into phosphoinositide 3-kinase catalysis and signalling , 1999, Nature.

[71]  S. Taylor,et al.  Role of the Glycine Triad in the ATP-binding Site of cAMP-dependent Protein Kinase* , 1997, The Journal of Biological Chemistry.

[72]  L. Johnson,et al.  Active and Inactive Protein Kinases: Structural Basis for Regulation , 1996, Cell.

[73]  S. Hubbard,et al.  Crystal structure of the tyrosine kinase domain of the human insulin receptor , 1994, Nature.

[74]  J. Zheng,et al.  Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. , 1991, Science.

[75]  C. Gibbs,et al.  Rational scanning mutagenesis of a protein kinase identifies functional regions involved in catalysis and substrate interactions. , 1991, The Journal of biological chemistry.

[76]  C. Sander,et al.  Database of homology‐derived protein structures and the structural meaning of sequence alignment , 1991, Proteins.

[77]  Albert J. Kooistra,et al.  1.15 – Structural Chemogenomics Databases to Navigate Protein–Ligand Interaction Space , 2017 .

[78]  M. Zvelebil,et al.  Activation loop sequences confer substrate specificity to phosphoinositide 3-kinase alpha (PI3Kalpha ). Functions of lipid kinase-deficient PI3Kalpha in signaling. , 2001, The Journal of biological chemistry.

[79]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..