Protein kinase inhibitors: structural insights into selectivity.

Protein kinases are involved in many diseases like cancer, inflammation, cardiovascular disease, and diabetes. They have become attractive target classes for drug development, making kinase inhibitors as important class of therapeutics. The success of small-molecule ATP-competitive kinase inhibitors such as Gleevec, Iressa, and Tarceva has attracted much attention in the recent past. Kinases make use of ATP for phosphorylation of a specific residue(s) on their protein substrates. More than 400 X-ray structures of about 70 different kinases are publicly available. These structures provide insights into selectivity and mechanisms of inhibition. However, prediction of binding specificity of kinase inhibitors based on structural information alone appears to be insufficient. Here, we will review these observations to gain insights into the rules that govern protein kinase inhibitor selectivity.

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

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

[3]  E. Goldsmith,et al.  Structural basis of inhibitor selectivity in MAP kinases. , 1998, Structure.

[4]  Gautam R. Desiraju,et al.  The Weak Hydrogen Bond: In Structural Chemistry and Biology , 1999 .

[5]  S. Parsons,et al.  c-Src, receptor tyrosine kinases, and human cancer. , 1999, Advances in cancer research.

[6]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[7]  L. Kuyper,et al.  Binding mode of the 4-anilinoquinazoline class of protein kinase inhibitor: X-ray crystallographic studies of 4-anilinoquinazolines bound to cyclin-dependent kinase 2 and p38 kinase. , 2000, Journal of medicinal chemistry.

[8]  David W. Anderson,et al.  SP600125, an anthrapyrazolone inhibitor of Jun N-terminal kinase , 2001, Proceedings of the National Academy of Sciences of the United States of America.

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

[10]  J. Kuriyan,et al.  Multiple BCR-ABL kinase domain mutations confer polyclonal resistance to the tyrosine kinase inhibitor imatinib (STI571) in chronic phase and blast crisis chronic myeloid leukemia. , 2002, Cancer cell.

[11]  S. Wedge,et al.  Novel 4-anilinoquinazolines with C-7 basic side chains: design and structure activity relationship of a series of potent, orally active, VEGF receptor tyrosine kinase inhibitors. , 2002, Journal of medicinal chemistry.

[12]  M. Sliwkowski,et al.  Structure of the Epidermal Growth Factor Receptor Kinase Domain Alone and in Complex with a 4-Anilinoquinazoline Inhibitor* , 2002, The Journal of Biological Chemistry.

[13]  L. Tong,et al.  Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site , 2002, Nature Structural Biology.

[14]  S. Hubbard Protein tyrosine kinases: autoregulation and small-molecule inhibition. , 2002, Current opinion in structural biology.

[15]  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.

[16]  D. Boschelli,et al.  SKI-606, a 4-anilino-3-quinolinecarbonitrile dual inhibitor of Src and Abl kinases, is a potent antiproliferative agent against chronic myelogenous leukemia cells in culture and causes regression of K562 xenografts in nude mice. , 2003, Cancer research.

[17]  A. Clerk,et al.  Kinases as therapeutic targets for heart failure , 2003, Nature Reviews Drug Discovery.

[18]  J. Lisnock,et al.  The structure of JNK3 in complex with small molecule inhibitors: structural basis for potency and selectivity. , 2003, Chemistry & biology.

[19]  D. Zaller,et al.  Structural basis for p38α MAP kinase quinazolinone and pyridol-pyrimidine inhibitor specificity , 2003, Nature Structural Biology.

[20]  H. Serve,et al.  A Single Amino Acid Exchange Inverts Susceptibility of Related Receptor Tyrosine Kinases for the ATP Site Inhibitor STI-571* 210 , 2003, The Journal of Biological Chemistry.

[21]  S. Gabriel,et al.  EGFR Mutations in Lung Cancer: Correlation with Clinical Response to Gefitinib Therapy , 2004, Science.

[22]  A. Ullrich,et al.  Strategies to overcome resistance to targeted protein kinase inhibitors , 2004, Nature Reviews Drug Discovery.

[23]  Krystal J Alligood,et al.  A Unique Structure for Epidermal Growth Factor Receptor Bound to GW572016 (Lapatinib) , 2004, Cancer Research.

[24]  David Bebbington,et al.  VX-680, a potent and selective small-molecule inhibitor of the Aurora kinases, suppresses tumor growth in vivo , 2004, Nature Medicine.

[25]  J. Mestan,et al.  Advances in the structural biology, design and clinical development of VEGF-R kinase inhibitors for the treatment of angiogenesis. , 2004, Biochimica et biophysica acta.

[26]  T. Clackson,et al.  Inhibition of wild-type and mutant Bcr-Abl by AP23464, a potent ATP-based oncogenic protein kinase inhibitor: implications for CML. , 2004, Blood.

[27]  K. Wilson,et al.  Structural Basis for the Autoinhibition and STI-571 Inhibition of c-Kit Tyrosine Kinase* , 2004, Journal of Biological Chemistry.

[28]  Stephen S. Taylor,et al.  Aurora-kinase inhibitors as anticancer agents , 2004, Nature Reviews Cancer.

[29]  J. Warmus,et al.  Structures of human MAP kinase kinase 1 (MEK1) and MEK2 describe novel noncompetitive kinase inhibition , 2004, Nature Structural &Molecular Biology.

[30]  P. Fischer,et al.  The design of drug candidate molecules as selective inhibitors of therapeutically relevant protein kinases. , 2004, Current medicinal chemistry.

[31]  D. Barford,et al.  Mechanism of Activation of the RAF-ERK Signaling Pathway by Oncogenic Mutations of B-RAF , 2004, Cell.

[32]  Karen Lackey,et al.  Synthesis and SAR of potent EGFR/erbB2 dual inhibitors. , 2004, Bioorganic & medicinal chemistry letters.

[33]  L. Johnson,et al.  Protein Kinase Inhibitors: Insights into Drug Design from Structure , 2004, Science.

[34]  Ping Chen,et al.  Discovery of N-(2-chloro-6-methyl- phenyl)-2-(6-(4-(2-hydroxyethyl)- piperazin-1-yl)-2-methylpyrimidin-4- ylamino)thiazole-5-carboxamide (BMS-354825), a dual Src/Abl kinase inhibitor with potent antitumor activity in preclinical assays. , 2004, Journal of medicinal chemistry.

[35]  Benoit Roux,et al.  On the Importance of Atomic Fluctuations, Protein Flexibility, and Solvent in Ion Permeation , 2004, The Journal of general physiology.

[36]  D. Williams,et al.  Recent kinase and kinase inhibitor X-ray structures: mechanisms of inhibition and selectivity insights. , 2004, Current medicinal chemistry.

[37]  John G Cumming,et al.  Novel, potent and selective anilinoquinazoline and anilinopyrimidine inhibitors of p38 MAP kinase. , 2004, Bioorganic & medicinal chemistry letters.

[38]  T J Stout,et al.  High-throughput structural biology in drug discovery: protein kinases. , 2004, Current pharmaceutical design.

[39]  Susan S. Taylor,et al.  Regulation of protein kinases; controlling activity through activation segment conformation. , 2004, Molecular cell.

[40]  Sam-Yong Park,et al.  Structural basis for the selective inhibition of JNK1 by the scaffolding protein JIP1 and SP600125 , 2004, The EMBO journal.

[41]  F. Lu,et al.  The structural basis for autoinhibition of FLT3 by the juxtamembrane domain. , 2004, Molecular cell.

[42]  C. Sawyers,et al.  Comparative analysis of two clinically active BCR-ABL kinase inhibitors reveals the role of conformation-specific binding in resistance. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[43]  J. Mestan,et al.  Advances in the structural biology, design and clinical development of Bcr-Abl kinase inhibitors for the treatment of chronic myeloid leukaemia. , 2005, Biochimica et biophysica acta.

[44]  William Pao,et al.  Inhibition of drug-resistant mutants of ABL, KIT, and EGF receptor kinases. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[45]  L. Wodicka,et al.  A small molecule–kinase interaction map for clinical kinase inhibitors , 2005, Nature Biotechnology.

[46]  Matthew R. Lee,et al.  MAP Kinase p38Inhibitors: Clinical Results and an Intimate Look at Their Interactions with p38α Protein , 2005 .

[47]  Hiroshi Hirai,et al.  Recent advances in the development of selective small molecule inhibitors for cyclin-dependent kinases. , 2005, Current topics in medicinal chemistry.

[48]  Christopher W Murray,et al.  Identification of novel p38alpha MAP kinase inhibitors using fragment-based lead generation. , 2005, Journal of medicinal chemistry.

[49]  Britt-Marie Swahn,et al.  Design and synthesis of 6-anilinoindazoles as selective inhibitors of c-Jun N-terminal kinase-3. , 2005, Bioorganic & medicinal chemistry letters.

[50]  E. Scholar,et al.  Role of Tyrosine Kinase Inhibitors in Cancer Therapy , 2005, Journal of Pharmacology and Experimental Therapeutics.

[51]  A. Vulpetti,et al.  Potent and selective Aurora inhibitors identified by the expansion of a novel scaffold for protein kinase inhibition. , 2005, Journal of medicinal chemistry.

[52]  Yoshihisa Suzuki,et al.  Crystal structures of proto-oncogene kinase Pim1: a target of aberrant somatic hypermutations in diffuse large cell lymphoma. , 2005, Journal of molecular biology.

[53]  J. Drevs,et al.  Receptor tyrosine kinases and anticancer therapy. , 2005, Current pharmaceutical design.

[54]  Paul D. Johnson,et al.  5-Substituted 4-anilinoquinazolines as potent, selective and orally active inhibitors of erbB2 receptor tyrosine kinase. , 2005, Bioorganic & medicinal chemistry letters.

[55]  Ram Thaimattam,et al.  3D-QSAR studies on c-Src kinase inhibitors and docking analyses of a potent dual kinase inhibitor of c-Src and c-Abl kinases. , 2005, Bioorganic & medicinal chemistry.

[56]  New heterocyclic analogues of 4-(2-chloro-5-methoxyanilino)quinazolines as potent and selective c-Src kinase inhibitors. , 2005, Bioorganic & medicinal chemistry letters.

[57]  Donna Neuberg,et al.  Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl. , 2005, Cancer cell.

[58]  M. Fleming,et al.  Pim-1 Ligand-bound Structures Reveal the Mechanism of Serine/Threonine Kinase Inhibition by LY294002* , 2005, Journal of Biological Chemistry.

[59]  N. Keen,et al.  Progress in the development of selective inhibitors of aurora kinases. , 2005, Current topics in medicinal chemistry.

[60]  Peter M Fischer,et al.  Strategies for the design of potent and selective kinase inhibitors. , 2005, Current pharmaceutical design.

[61]  R. Berro,et al.  Potential use of pharmacological cyclin-dependent kinase inhibitors as anti-HIV therapeutics. , 2006, Current pharmaceutical design.

[62]  Daniel K. Treiber,et al.  Structure of the kinase domain of an imatinib-resistant Abl mutant in complex with the Aurora kinase inhibitor VX-680. , 2006, Cancer research.

[63]  Paul D. Johnson,et al.  Inhibitors of epidermal growth factor receptor tyrosine kinase: Novel C-5 substituted anilinoquinazolines designed to target the ribose pocket. , 2006, Bioorganic & medicinal chemistry letters.

[64]  C. Peifer,et al.  New approaches to the treatment of inflammatory disorders small molecule inhibitors of p38 MAP kinase. , 2006, Current topics in medicinal chemistry.

[65]  J. Breed,et al.  SAR and inhibitor complex structure determination of a novel class of potent and specific Aurora kinase inhibitors. , 2006, Bioorganic & medicinal chemistry letters.

[66]  J. Bischoff,et al.  3-Amino-1,4,5,6-tetrahydropyrrolo[3,4-c]pyrazoles: a new class of CDK2 inhibitors. , 2006, Bioorganic & medicinal chemistry letters.