51
|
Singh SK, Hasan SS, Zakharov SD, Naurin S, Cohn W, Ma J, Whitelegge JP, Cramer WA. Trans-membrane Signaling in Photosynthetic State Transitions: REDOX- AND STRUCTURE-DEPENDENT INTERACTION IN VITRO BETWEEN STT7 KINASE AND THE CYTOCHROME b6f COMPLEX. J Biol Chem 2016; 291:21740-21750. [PMID: 27539852 DOI: 10.1074/jbc.m116.732545] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 08/01/2016] [Indexed: 12/11/2022] Open
Abstract
Trans-membrane signaling involving a serine/threonine kinase (Stt7 in Chlamydomonas reinhardtii) directs light energy distribution between the two photosystems of oxygenic photosynthesis. Oxidation of plastoquinol mediated by the cytochrome b6f complex on the electrochemically positive side of the thylakoid membrane activates the kinase domain of Stt7 on the trans (negative) side, leading to phosphorylation and redistribution ("state transition") of the light-harvesting chlorophyll proteins between the two photosystems. The molecular description of the Stt7 kinase and its interaction with the cytochrome b6f complex are unknown or unclear. In this study, Stt7 kinase has been cloned, expressed, and purified in a heterologous host. Stt7 kinase is shown to be active in vitro in the presence of reductant and purified as a tetramer, as determined by analytical ultracentrifugation, electron microscopy, and electrospray ionization mass spectrometry, with a molecular weight of 332 kDa, consisting of an 83.41-kDa monomer. Far-UV circular dichroism spectra show Stt7 to be mostly α-helical and document a physical interaction with the b6f complex through increased thermal stability of Stt7 secondary structure. The activity of wild-type Stt7 and its Cys-Ser mutant at positions 68 and 73 in the presence of a reductant suggest that the enzyme does not require a disulfide bridge for its activity as suggested elsewhere. Kinase activation in vivo could result from direct interaction between Stt7 and the b6f complex or long-range reduction of Stt7 by superoxide, known to be generated in the b6f complex by quinol oxidation.
Collapse
Affiliation(s)
| | | | | | | | - Whitaker Cohn
- the Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90024
| | - Jia Ma
- Biophysical Analysis Laboratory, Bindley Bioscience Center,Purdue University, West Lafayette, Indiana 47907 and
| | - Julian P Whitelegge
- the Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90024
| | | |
Collapse
|
52
|
Zhang ZM, Ma KW, Yuan S, Luo Y, Jiang S, Hawara E, Pan S, Ma W, Song J. Structure of a pathogen effector reveals the enzymatic mechanism of a novel acetyltransferase family. Nat Struct Mol Biol 2016; 23:847-52. [PMID: 27525589 DOI: 10.1038/nsmb.3279] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/19/2016] [Indexed: 02/07/2023]
Abstract
Effectors secreted by the type III secretion system are essential for bacterial pathogenesis. Members of the Yersinia outer-protein J (YopJ) family of effectors found in diverse plant and animal pathogens depend on a protease-like catalytic triad to acetylate host proteins and produce virulence. However, the structural basis for this noncanonical acetyltransferase activity remains unknown. Here, we report the crystal structures of the YopJ effector HopZ1a, produced by the phytopathogen Pseudomonas syringae, in complex with the eukaryote-specific cofactor inositol hexakisphosphate (IP6) and/or coenzyme A (CoA). Structural, computational and functional characterizations reveal a catalytic core with a fold resembling that of ubiquitin-like cysteine proteases and an acetyl-CoA-binding pocket formed after IP6-induced structural rearrangements. Modeling-guided mutagenesis further identified key IP6-interacting residues of Salmonella effector AvrA that are required for acetylating its substrate. Our study reveals the structural basis of a novel class of acetyltransferases and the conserved allosteric regulation of YopJ effectors by IP6.
Collapse
Affiliation(s)
- Zhi-Min Zhang
- Department of Biochemistry, University of California, Riverside, Riverside, California, USA
| | - Ka-Wai Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, California, USA
| | - Shuguang Yuan
- Laboratory of Physical Chemistry of Polymers and Membranes, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Youfu Luo
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Shushu Jiang
- Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, California, USA
| | - Eva Hawara
- Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, California, USA
| | - Songqin Pan
- Center for Plant Cell Biology, University of California, Riverside, Riverside, California, USA
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, California, USA.,Center for Plant Cell Biology, University of California, Riverside, Riverside, California, USA.,Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, Riverside, California, USA
| |
Collapse
|
53
|
Petrvalska O, Kosek D, Kukacka Z, Tosner Z, Man P, Vecer J, Herman P, Obsilova V, Obsil T. Structural Insight into the 14-3-3 Protein-dependent Inhibition of Protein Kinase ASK1 (Apoptosis Signal-regulating kinase 1). J Biol Chem 2016; 291:20753-65. [PMID: 27514745 DOI: 10.1074/jbc.m116.724310] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 11/06/2022] Open
Abstract
Apoptosis signal-regulating kinase 1 (ASK1, also known as MAP3K5), a member of the mitogen-activated protein kinase kinase kinase (MAP3K) family, regulates diverse physiological processes. The activity of ASK1 is triggered by various stress stimuli and is involved in the pathogenesis of cancer, neurodegeneration, inflammation, and diabetes. ASK1 forms a high molecular mass complex whose activity is, under non-stress conditions, suppressed through interaction with thioredoxin and the scaffolding protein 14-3-3. The 14-3-3 protein binds to the phosphorylated Ser-966 motif downstream of the ASK1 kinase domain. The role of 14-3-3 in the inhibition of ASK1 has yet to be elucidated. In this study we performed structural analysis of the complex between the ASK1 kinase domain phosphorylated at Ser-966 (pASK1-CD) and the 14-3-3ζ protein. Small angle x-ray scattering (SAXS) measurements and chemical cross-linking revealed that the pASK1-CD·14-3-3ζ complex is dynamic and conformationally heterogeneous. In addition, structural analysis coupled with the results of phosphorus NMR and time-resolved tryptophan fluorescence measurements suggest that 14-3-3ζ interacts with the kinase domain of ASK1 in close proximity to its active site, thus indicating this interaction might block its accessibility and/or affect its conformation.
Collapse
Affiliation(s)
- Olivia Petrvalska
- From the Department of Physical and Macromolecular Chemistry, Faculty of Science, and Institute of Physiology and
| | - Dalibor Kosek
- From the Department of Physical and Macromolecular Chemistry, Faculty of Science, and Institute of Physiology and
| | - Zdenek Kukacka
- the Institute of Microbiology, The Czech Academy of Sciences, 14220 Prague, and
| | - Zdenek Tosner
- From the Department of Physical and Macromolecular Chemistry, Faculty of Science, and
| | - Petr Man
- the Institute of Microbiology, The Czech Academy of Sciences, 14220 Prague, and Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague
| | - Jaroslav Vecer
- the Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, 12116 Prague, Czech Republic
| | - Petr Herman
- the Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, 12116 Prague, Czech Republic
| | | | - Tomas Obsil
- From the Department of Physical and Macromolecular Chemistry, Faculty of Science, and Institute of Physiology and
| |
Collapse
|
54
|
Kwarcinski FE, Brandvold KR, Phadke S, Beleh OM, Johnson TK, Meagher JL, Seeliger MA, Stuckey JA, Soellner MB. Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity. ACS Chem Biol 2016; 11:1296-304. [PMID: 26895387 PMCID: PMC7306399 DOI: 10.1021/acschembio.5b01018] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the kinase field, there are many widely held tenets about conformation-selective inhibitors that have yet to be validated using controlled experiments. We have designed, synthesized, and characterized a series of kinase inhibitor analogues of dasatinib, an FDA-approved kinase inhibitor that binds the active conformation. This inhibitor series includes two Type II inhibitors that bind the DFG-out inactive conformation and two inhibitors that bind the αC-helix-out inactive conformation. Using this series of compounds, we analyze the impact that conformation-selective inhibitors have on target binding and kinome-wide selectivity.
Collapse
Affiliation(s)
- Frank E. Kwarcinski
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Sameer Phadke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Omar M. Beleh
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Taylor K. Johnson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794
| | - Jeanne A. Stuckey
- Center for Structural Biology, University of Michigan, Ann Arbor, MI 48109
| | - Matthew B. Soellner
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| |
Collapse
|
55
|
Saha S, Paul A, Herring L, Dutta A, Bhattacharya A, Samaddar S, Goshe MB, DasGupta M. Gatekeeper Tyrosine Phosphorylation of SYMRK Is Essential for Synchronizing the Epidermal and Cortical Responses in Root Nodule Symbiosis. PLANT PHYSIOLOGY 2016; 171:71-81. [PMID: 26960732 PMCID: PMC4854696 DOI: 10.1104/pp.15.01962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/09/2016] [Indexed: 05/04/2023]
Abstract
Symbiosis receptor kinase (SYMRK) is indispensable for activation of root nodule symbiosis (RNS) at both epidermal and cortical levels and is functionally conserved in legumes. Previously, we reported SYMRK to be phosphorylated on "gatekeeper" Tyr both in vitro as well as in planta. Since gatekeeper phosphorylation was not necessary for activity, the significance remained elusive. Herein, we show that substituting gatekeeper with nonphosphorylatable residues like Phe or Ala significantly affected autophosphorylation on selected targets on activation segment/αEF and β3-αC loop of SYMRK. In addition, the same gatekeeper mutants failed to restore proper symbiotic features in a symrk null mutant where rhizobial invasion of the epidermis and nodule organogenesis was unaffected but rhizobia remain restricted to the epidermis in infection threads migrating parallel to the longitudinal axis of the root, resulting in extensive infection patches at the nodule apex. Thus, gatekeeper phosphorylation is critical for synchronizing epidermal/cortical responses in RNS.
Collapse
Affiliation(s)
- Sudip Saha
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (S. Saha, A.P., A.D., A.B., S. Samaddar, M.D.); andDepartment of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695 (L.H., M.B.G.)
| | - Anindita Paul
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (S. Saha, A.P., A.D., A.B., S. Samaddar, M.D.); andDepartment of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695 (L.H., M.B.G.)
| | - Laura Herring
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (S. Saha, A.P., A.D., A.B., S. Samaddar, M.D.); andDepartment of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695 (L.H., M.B.G.)
| | - Ayan Dutta
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (S. Saha, A.P., A.D., A.B., S. Samaddar, M.D.); andDepartment of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695 (L.H., M.B.G.)
| | - Avisek Bhattacharya
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (S. Saha, A.P., A.D., A.B., S. Samaddar, M.D.); andDepartment of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695 (L.H., M.B.G.)
| | - Sandip Samaddar
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (S. Saha, A.P., A.D., A.B., S. Samaddar, M.D.); andDepartment of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695 (L.H., M.B.G.)
| | - Michael B Goshe
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (S. Saha, A.P., A.D., A.B., S. Samaddar, M.D.); andDepartment of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695 (L.H., M.B.G.)
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (S. Saha, A.P., A.D., A.B., S. Samaddar, M.D.); andDepartment of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695 (L.H., M.B.G.)
| |
Collapse
|
56
|
Mondal J, Tiwary P, Berne BJ. How a Kinase Inhibitor Withstands Gatekeeper Residue Mutations. J Am Chem Soc 2016; 138:4608-15. [DOI: 10.1021/jacs.6b01232] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jagannath Mondal
- Tata Institute
of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, India
| | - Pratyush Tiwary
- Department
of Chemistry, Columbia University, New York, New York 10027, United States
| | - B. J. Berne
- Department
of Chemistry, Columbia University, New York, New York 10027, United States
| |
Collapse
|
57
|
Bosc N, Wroblowski B, Aci-Sèche S, Meyer C, Bonnet P. A Proteometric Analysis of Human Kinome: Insight into Discriminant Conformation-dependent Residues. ACS Chem Biol 2015; 10:2827-40. [PMID: 26411811 DOI: 10.1021/acschembio.5b00555] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Because of the success of imatinib, the first type-II kinase inhibitor approved by the FDA in 2001, sustained efforts have been made by the pharmaceutical industry to discover novel compounds stabilizing the inactive conformation of protein kinases. On the seven type-II inhibitors having reached the market, four were released in 2012, suggesting an acceleration of the research of such a class of compounds. Still, they represent less than a third of the protein kinase inhibitors available to patients today. The identification of key residues involved in the binding of this type of ligands in the kinase active site might ease the design of potent and selective type-II inhibitors. In order to identify those discriminant residues, we have developed a proteometric approach combining residue descriptors of protein kinase sequences and biological activities of various type-II kinase inhibitors. We applied Partial Least Squares (PLS) regression to identify 29 key residues that influence the binding of four type-II inhibitors to most proteins of the kinome. The gatekeeper residue was found to be the most relevant, confirming an essential role in ligand binding as well as in protein kinase conformational changes. Using the newly developed proteometric model, we predicted the propensity of each protein kinase to be inhibited by type-II ligands. The model was further validated using an external data set of protein/ligand activity pairs. Other residues present in the kinase domain, and more specifically in the binding site, have been highlighted by this approach, but their role in biological mechanisms is still unknown.
Collapse
Affiliation(s)
- Nicolas Bosc
- Institut
de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d’Orléans 7311, Université d’Orléans
BP 6759, 45067 Orléans
Cedex 2, France
| | - Berthold Wroblowski
- Janssen Research & Development, a division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Samia Aci-Sèche
- Institut
de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d’Orléans 7311, Université d’Orléans
BP 6759, 45067 Orléans
Cedex 2, France
| | - Christophe Meyer
- Centre de Recherche Janssen-Cilag, Campus de Maigremont - CS
10615, 27106 Val de
Reuil Cedex, France
| | - Pascal Bonnet
- Institut
de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d’Orléans 7311, Université d’Orléans
BP 6759, 45067 Orléans
Cedex 2, France
| |
Collapse
|
58
|
Alexander LT, Möbitz H, Drueckes P, Savitsky P, Fedorov O, Elkins JM, Deane CM, Cowan-Jacob SW, Knapp S. Type II Inhibitors Targeting CDK2. ACS Chem Biol 2015; 10:2116-25. [PMID: 26158339 DOI: 10.1021/acschembio.5b00398] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Kinases can switch between active and inactive conformations of the ATP/Mg(2+) binding motif DFG, which has been explored for the development of type I or type II inhibitors. However, factors modulating DFG conformations remain poorly understood. We chose CDK2 as a model system to study the DFG in-out transition on a target that was thought to have an inaccessible DFG-out conformation. We used site-directed mutagenesis of key residues identified in structural comparisons in conjunction with biochemical and biophysical characterization of the generated mutants. As a result, we identified key residues that facilitate the DFG-out movement, facilitating binding of type II inhibitors. However, surprisingly, we also found that wild type CDK2 is able to bind type II inhibitors. Using protein crystallography structural analysis of the CDK2 complex with an aminopyrimidine-phenyl urea inhibitor (K03861) revealed a canonical type II binding mode and the first available type II inhibitor CDK2 cocrystal structure. We found that the identified type II inhibitors compete with binding of activating cyclins. In addition, analysis of the binding kinetics of the identified inhibitors revealed slow off-rates. The study highlights the importance of residues that may be distant to the ATP binding pocket in modulating the energetics of the DFG-out transition and hence inhibitor binding. The presented data also provide the foundation for a new class of slow off-rate cyclin-competitive CDK2 inhibitors targeting the inactive DFG-out state of this important kinase target.
Collapse
Affiliation(s)
- Leila T. Alexander
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom
| | - Henrik Möbitz
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Peter Drueckes
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Pavel Savitsky
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Oleg Fedorov
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
| | - Jonathan M. Elkins
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
| | - Charlotte M. Deane
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom
| | - Sandra W. Cowan-Jacob
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Stefan Knapp
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str.
9, D-60438 Frankfurt
am Main, Germany
| |
Collapse
|
59
|
Abstract
Protein tyrosine kinases differ widely in their propensity to undergo rearrangements
of the N-terminal Asp–Phe–Gly (DFG) motif of the activation
loop, with some, including FGFR1 kinase, appearing refractory to this so-called
‘DFG flip'. Recent inhibitor-bound structures have unexpectedly
revealed FGFR1 for the first time in a ‘DFG-out' state. Here we
use conformationally selective inhibitors as chemical probes for interrogation of
the structural and dynamic features that appear to govern the DFG flip in FGFR1. Our
detailed structural and biophysical insights identify contributions from altered
dynamics in distal elements, including the αH helix, towards the
outstanding stability of the DFG-out complex with the inhibitor ponatinib. We
conclude that the αC-β4 loop and ‘molecular
brake' regions together impose a high energy barrier for this
conformational rearrangement, and that this may have significance for maintaining
autoinhibition in the non-phosphorylated basal state of FGFR1. Receptor tyrosine kinases are key mediators of cell proliferation
that have been implicated in several disease states for which they represent promising
drug targets. Here the authors determine the thermodynamic basis for the low propensity
of FGFR1 to access the DFG-Phe-out conformation required to bind type-II
inhibitors.
Collapse
|
60
|
Gross S, Rahal R, Stransky N, Lengauer C, Hoeflich KP. Targeting cancer with kinase inhibitors. J Clin Invest 2015; 125:1780-9. [PMID: 25932675 DOI: 10.1172/jci76094] [Citation(s) in RCA: 307] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Kinase inhibitors have played an increasingly prominent role in the treatment of cancer and other diseases. Currently, more than 25 oncology drugs that target kinases have been approved, and numerous additional therapeutics are in various stages of clinical evaluation. In this Review, we provide an in-depth analysis of activation mechanisms for kinases in cancer, highlight recent successes in drug discovery, and demonstrate the clinical impact of selective kinase inhibitors. We also describe the substantial progress that has been made in designing next-generation inhibitors to circumvent on-target resistance mechanisms, as well as ongoing strategies for combining kinase inhibitors in the clinic. Last, there are numerous prospects for the discovery of novel kinase targets, and we explore cancer immunotherapy as a new and promising research area for studying kinase biology.
Collapse
|
61
|
Snape TJ, Warr T. Approaches toward improving the prognosis of pediatric patients with glioma: pursuing mutant drug targets with emerging small molecules. Semin Pediatr Neurol 2015; 22:28-34. [PMID: 25976258 DOI: 10.1016/j.spen.2014.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gliomas represent approximately 70% of all pediatric brain tumors, and most of these are of astrocytic lineage; furthermore, malignant or high-grade astrocytomas account for approximately 20% of pediatric astrocytoma. Treatment options for pediatric patients with glioma are limited. Although low-grade astrocytomas are relatively slow-growing tumors that can often be cured through surgical resection, a significant proportion of cases recur, as such, new treatments are desperately needed. This review covers the various approaches that are currently being made toward improving the prognosis of pediatric patients with glioma by pursuing pediatric-selective mutant drug targets with emerging small molecules.
Collapse
Affiliation(s)
- Timothy J Snape
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Lancashire, UK.
| | - Tracy Warr
- Brain Tumour Research Centre, University of Wolverhampton, Wolverhampton, UK
| |
Collapse
|
62
|
Sandberg RB, Banchelli M, Guardiani C, Menichetti S, Caminati G, Procacci P. Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations. J Chem Theory Comput 2015; 11:423-35. [DOI: 10.1021/ct500964e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Robert B. Sandberg
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York 13902, United States
| | | | - Carlo Guardiani
- Department
of Physics, University of Cagliari, 09124 Cagliari, Italy
- IOM Institute, CNR, 09042 Cagliari, Italy
| | | | | | | |
Collapse
|
63
|
Ung PMU, Schlessinger A. DFGmodel: predicting protein kinase structures in inactive states for structure-based discovery of type-II inhibitors. ACS Chem Biol 2015; 10:269-78. [PMID: 25420233 PMCID: PMC4301084 DOI: 10.1021/cb500696t] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein kinases exist in equilibrium of active and inactive states, in which the aspartate-phenylalanine-glycine motif in the catalytic domain undergoes conformational changes that are required for function. Drugs targeting protein kinases typically bind the primary ATP-binding site of an active state (type-I inhibitors) or utilize an allosteric pocket adjacent to the ATP-binding site in the inactive state (type-II inhibitors). Limited crystallographic data of protein kinases in the inactive state hampers the application of rational drug discovery methods for developing type-II inhibitors. Here, we present a computational approach to generate structural models of protein kinases in the inactive conformation. We first perform a comprehensive analysis of all protein kinase structures deposited in the Protein Data Bank. We then develop DFGmodel, a method that takes either a known structure of a kinase in the active conformation or a sequence of a kinase without a structure, to generate kinase models in the inactive conformation. Evaluation of DFGmodel's performance using various measures indicates that the inactive kinase models are accurate, exhibiting RMSD of 1.5 Å or lower. The kinase models also accurately distinguish type-II kinase inhibitors from likely nonbinders (AUC > 0.70), suggesting that they are useful for virtual screening. Finally, we demonstrate the applicability of our approach with three case studies. For example, the models are able to capture inhibitors with unintended off-target activity. Our computational approach provides a structural framework for chemical biologists to characterize kinases in the inactive state and to explore new chemical spaces with structure-based drug design.
Collapse
Affiliation(s)
- Peter Man-Un Ung
- Department of Pharmacology
and Systems Therapeutics, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Avner Schlessinger
- Department of Pharmacology
and Systems Therapeutics, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| |
Collapse
|
64
|
Abstract
The quest for ever more selective kinase inhibitors as potential future drugs has yielded a large repertoire of chemical probes that are selective for specific kinase conformations. These probes have been useful tools to obtain structural snapshots of kinase conformational plasticity. Similarly, kinetic and thermodynamic inhibitor binding experiments provide glimpses at the time scales and energetics of conformational interconversions. These experimental insights are complemented by computational predictions of conformational energy landscapes and simulations of conformational transitions and of the process of inhibitors binding to the protein kinase domain. A picture emerges in which highly selective inhibitors capitalize on the dynamic nature of kinases.
Collapse
Affiliation(s)
- Michael Tong
- Department
of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| |
Collapse
|
65
|
Vijayan RSK, He P, Modi V, Duong-Ly KC, Ma H, Peterson JR, Dunbrack RL, Levy RM. Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. J Med Chem 2014; 58:466-79. [PMID: 25478866 PMCID: PMC4326797 DOI: 10.1021/jm501603h] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Structural
coverage of the human kinome has been steadily increasing
over time. The structures provide valuable insights into the molecular
basis of kinase function and also provide a foundation for understanding
the mechanisms of kinase inhibitors. There are a large number of kinase
structures in the PDB for which the Asp and Phe of the DFG motif on
the activation loop swap positions, resulting in the formation of
a new allosteric pocket. We refer to these structures as “classical
DFG-out” conformations in order to distinguish them from conformations
that have also been referred to as DFG-out in the literature but that
do not have a fully formed allosteric pocket. We have completed a
structural analysis of almost 200 small molecule inhibitors bound
to classical DFG-out conformations; we find that they are recognized
by both type I and type II inhibitors. In contrast, we find that nonclassical
DFG-out conformations strongly select against type II inhibitors because
these structures have not formed a large enough allosteric pocket
to accommodate this type of binding mode. In the course of this study
we discovered that the number of structurally validated type II inhibitors
that can be found in the PDB and that are also represented in publicly
available biochemical profiling studies of kinase inhibitors is very
small. We have obtained new profiling results for several additional
structurally validated type II inhibitors identified through our conformational
analysis. Although the available profiling data for type II inhibitors
is still much smaller than for type I inhibitors, a comparison of
the two data sets supports the conclusion that type II inhibitors
are more selective than type I. We comment on the possible contribution
of the DFG-in to DFG-out conformational reorganization to the selectivity.
Collapse
Affiliation(s)
- R S K Vijayan
- Center for Biophysics & Computational Biology and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States
| | | | | | | | | | | | | | | |
Collapse
|
66
|
Rudolph J, Xiao Y, Pardi A, Ahn NG. Slow inhibition and conformation selective properties of extracellular signal-regulated kinase 1 and 2 inhibitors. Biochemistry 2014; 54:22-31. [PMID: 25350931 DOI: 10.1021/bi501101v] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The mitogen-activated protein (MAP) kinase pathway is a target for anticancer therapy, validated using inhibitors of B-Raf and MAP kinase kinase (MKK) 1 and 2. Clinical outcomes show a high frequency of acquired resistance in patient tumors, involving upregulation of activity of the MAP kinase, extracellular signal-regulated kinase (ERK) 1 and 2. Thus, inhibitors for ERK1/2 are potentially important for targeted therapeutics against cancer. The structures and potencies of different ERK inhibitors have been published, but their kinetic mechanisms have not been characterized. Here we perform enzyme kinetic studies on six representative ERK inhibitors, with potencies varying from 100 pM to 20 μM. Compounds with significant biological activity (IC50 < 100 nM) that inhibit in the subnanomolar range (Vertex-11e and SCH772984) display slow-onset inhibition and represent the first inhibitors of ERK2 known to demonstrate slow dissociation rate constants (values of 0.2 and 1.1 h(-1), respectively). Furthermore, we demonstrate using kinetic competition assays that Vertex-11e binds with differing affinities to ERK2 in its inactive, unphosphorylated and active, phosphorylated forms. Finally, two-dimensional heteronuclear multiple-quantum correlation nuclear magnetic resonance experiments reveal that distinct conformational states are formed in complexes of Vertex-11e with inactive and active ERK2. Importantly, two conformers interconvert in equilibrium in the active ERK2 apoenzyme, but Vertex-11e strongly shifts the equilibrium completely to one conformer. Thus, a high-affinity, slow dissociation inhibitor stabilizes different enzyme conformations depending on the activity state of ERK2 and reveals properties of conformational selection toward the active kinase.
Collapse
Affiliation(s)
- Johannes Rudolph
- Department of Chemistry and Biochemistry, ‡Howard Hughes Medical Institute, and §BioFrontiers Institute, University of Colorado , Boulder, Colorado 80309, United States
| | | | | | | |
Collapse
|
67
|
Schmucker S, Sumara I. Molecular dynamics of PLK1 during mitosis. Mol Cell Oncol 2014; 1:e954507. [PMID: 27308323 PMCID: PMC4905186 DOI: 10.1080/23723548.2014.954507] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 12/30/2022]
Abstract
Polo-like kinase 1 (PLK1) is a key regulator of eukaryotic cell division. During mitosis, dynamic regulation of PLK1 is crucial for its roles in centrosome maturation, spindle assembly, microtubule–kinetochore attachment, and cytokinesis. Similar to other members of the PLK family, the molecular architecture of PLK1 protein is characterized by 2 domains—the kinase domain and the regulatory substrate-binding domain (polo-box domain)—that cooperate and control PLK1 function during mitosis. Mitotic cells employ many layers of regulation to activate and target PLK1 to different cellular structures in a timely manner. During the last decade, numerous studies have shed light on the precise molecular mechanisms orchestrating the mitotic activity of PLK1 in time and space. This review aims to discuss available data and concepts related to regulation of the molecular dynamics of human PLK1 during mitotic progression.
Collapse
Affiliation(s)
- Stephane Schmucker
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) ; Illkirch, France
| | - Izabela Sumara
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) ; Illkirch, France
| |
Collapse
|
68
|
Chaikuad A, Tacconi E, Zimmer J, Liang Y, Gray NS, Tarsounas M, Knapp S. A unique inhibitor binding site in ERK1/2 is associated with slow binding kinetics. Nat Chem Biol 2014; 10:853-60. [PMID: 25195011 PMCID: PMC4687050 DOI: 10.1038/nchembio.1629] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 08/05/2014] [Indexed: 01/07/2023]
Abstract
Activation of the ERK pathway is a hallmark of cancer, and targeting of upstream signaling partners led to the development of approved drugs. Recently, SCH772984 has been shown to be a selective and potent ERK1/2 inhibitor. Here we report the structural mechanism for its remarkable selectivity. In ERK1/2, SCH772984 induces a so-far-unknown binding pocket that accommodates the piperazine-phenyl-pyrimidine decoration. This new binding pocket was created by an inactive conformation of the phosphate-binding loop and an outward tilt of helix αC. In contrast, structure determination of SCH772984 with the off-target haspin and JNK1 revealed two canonical but distinct type I binding modes. Notably, the new binding mode with ERK1/2 was associated with slow binding kinetics in vitro as well as in cell-based assay systems. The described binding mode of SCH772984 with ERK1/2 enables the design of a new type of specific kinase inhibitors with prolonged on-target activity.
Collapse
Affiliation(s)
- Apirat Chaikuad
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Eliana Tacconi
- Telomere and Genome Stability Group, The CR-UK/MRC Oxford Institute for Radiation Oncology, Old Campus Road Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Jutta Zimmer
- Telomere and Genome Stability Group, The CR-UK/MRC Oxford Institute for Radiation Oncology, Old Campus Road Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Yanke Liang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Cancer Biology, Dana Farber Cancer Institute, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Nathanael S. Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Cancer Biology, Dana Farber Cancer Institute, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Madalena Tarsounas
- Telomere and Genome Stability Group, The CR-UK/MRC Oxford Institute for Radiation Oncology, Old Campus Road Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Stefan Knapp
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Department of Biochemistry & Molecular Medicine, George Washington University, Ross Hall, 2300 Eye Street NW, Washington, DC 20037, USA
| |
Collapse
|
69
|
Zhao Z, Wu H, Wang L, Liu Y, Knapp S, Liu Q, Gray NS. Exploration of type II binding mode: A privileged approach for kinase inhibitor focused drug discovery? ACS Chem Biol 2014; 9:1230-41. [PMID: 24730530 PMCID: PMC4068218 DOI: 10.1021/cb500129t] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
The ATP site of kinases displays
remarkable conformational flexibility
when accommodating chemically diverse small molecule inhibitors. The
so-called activation segment, whose conformation controls catalytic
activity and access to the substrate binding pocket, can undergo a
large conformational change with the active state assuming a ‘DFG-in’
and an inactive state assuming a ‘DFG-out’ conformation.
Compounds that preferentially bind to the DFG-out conformation are
typically called ‘type II’ inhibitors in contrast to ‘type
I’ inhibitors that bind to the DFG-in conformation. This review
surveys the large number of type II inhibitors that have been developed
and provides an analysis of their crystallographically determined
binding modes. Using a small library of type II inhibitors, we demonstrate
that more than 200 kinases can be targeted, suggesting that type II
inhibitors may not be intrinsically more selective than type I inhibitors.
Collapse
Affiliation(s)
- Zheng Zhao
- High
Magnetic Field Laboratory, Chinese Academy of Sciences, P.O. Box 1110, Hefei, Anhui 230031, P. R. China
| | - Hong Wu
- High
Magnetic Field Laboratory, Chinese Academy of Sciences, P.O. Box 1110, Hefei, Anhui 230031, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230036, P. R. China
| | - Li Wang
- High
Magnetic Field Laboratory, Chinese Academy of Sciences, P.O. Box 1110, Hefei, Anhui 230031, P. R. China
| | - Yi Liu
- Wellspring
Biosciences LLC, 3210
Merryfield Row, San Diego, California 92121, United States
| | - Stefan Knapp
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford OX3 7LD, United Kingdom
| | - Qingsong Liu
- High
Magnetic Field Laboratory, Chinese Academy of Sciences, P.O. Box 1110, Hefei, Anhui 230031, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230036, P. R. China
| | - Nathanael S. Gray
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, Massachussetts 02115, United States
| |
Collapse
|
70
|
Hari SB, Merritt EA, Maly DJ. Conformation-selective ATP-competitive inhibitors control regulatory interactions and noncatalytic functions of mitogen-activated protein kinases. ACTA ACUST UNITED AC 2014; 21:628-35. [PMID: 24704509 DOI: 10.1016/j.chembiol.2014.02.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 02/17/2014] [Accepted: 02/20/2014] [Indexed: 01/07/2023]
Abstract
Most potent protein kinase inhibitors act by competing with ATP to block the phosphotransferase activity of their targets. However, emerging evidence demonstrates that ATP-competitive inhibitors can affect kinase interactions and functions in ways beyond blocking catalytic activity. Here, we show that stabilizing alternative ATP-binding site conformations of the mitogen-activated protein kinases (MAPKs) p38α and Erk2 with ATP-competitive inhibitors differentially, and in some cases divergently, modulates the abilities of these kinases to interact with upstream activators and deactivating phosphatases. Conformation-selective ligands are also able to modulate Erk2's ability to allosterically activate the MAPK phosphatase DUSP6, highlighting how ATP-competitive ligands can control noncatalytic kinase functions. Overall, these studies underscore the relationship between the ATP-binding and regulatory sites of MAPKs and provide insight into how ATP-competitive ligands can be designed to confer graded control over protein kinase function.
Collapse
Affiliation(s)
- Sanjay B Hari
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Ethan A Merritt
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
71
|
Abstract
In this issue of Chemistry & Biology, Hari and colleagues show that two positions in kinase active sites, including the well-known "gatekeeper" residue, regulate "in" versus "out" conformations of the conserved "DFG" motif. These findings suggest yet another role for the gatekeeper residue.
Collapse
Affiliation(s)
- Daniel K Treiber
- KINOMEscan Division of DiscoveRx Corporation, 11180 Roselle Street, Suite D, San Diego, CA, 92121, USA.
| | | |
Collapse
|
72
|
Hari SB, Perera BGK, Ranjitkar P, Seeliger MA, Maly DJ. Conformation-selective inhibitors reveal differences in the activation and phosphate-binding loops of the tyrosine kinases Abl and Src. ACS Chem Biol 2013; 8:2734-43. [PMID: 24106839 DOI: 10.1021/cb400663k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, an increasingly diverse array of potent and selective inhibitors that target the ATP-binding sites of protein kinases have been developed. Many of these inhibitors, like the clinically approved drug imatinib (Gleevec), stabilize a specific catalytically inactive ATP-binding site conformation of their kinases targets. Imatinib is notable in that it is highly selective for its kinase target, Abl, over other closely related tyrosine kinases, such as Src. In addition, imatinib is highly sensitive to the phosphorylation state of Abl's activation loop, which is believed to be a general characteristic of all inhibitors that stabilize a similar inactive ATP-binding site conformation. In this report, we perform a systematic analysis of a diverse series of ATP-competitive inhibitors that stabilize a similar inactive ATP-binding site conformation as imatinib with the tyrosine kinases Src and Abl. In contrast to imatinib, many of these inhibitors have very similar potencies against Src and Abl. Furthermore, only a subset of this class of inhibitors is sensitive to the phosphorylation state of the activation loop of these kinases. In attempting to explain this observation, we have uncovered an unexpected correlation between Abl's activation loop and another flexible active site feature, called the phosphate-binding loop (p-loop). These studies shed light on how imatinib is able to obtain its high target selectivity and reveal how the conformational preference of flexible active site regions can vary between closely related kinases.
Collapse
Affiliation(s)
- Sanjay B. Hari
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - B. Gayani K. Perera
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Pratistha Ranjitkar
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York 11794, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
73
|
Anastassiadis T, Duong-Ly KC, Deacon SW, Lafontant A, Ma H, Devarajan K, Dunbrack RL, Wu J, Peterson JR. A highly selective dual insulin receptor (IR)/insulin-like growth factor 1 receptor (IGF-1R) inhibitor derived from an extracellular signal-regulated kinase (ERK) inhibitor. J Biol Chem 2013; 288:28068-77. [PMID: 23935097 PMCID: PMC3784719 DOI: 10.1074/jbc.m113.505032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Dual inhibitors of the closely related receptor tyrosine kinases insulin-like growth factor 1 receptor (IGF-1R) and insulin receptor (IR) are promising therapeutic agents in cancer. Here, we report an unusually selective class of dual inhibitors of IGF-1R and IR identified in a parallel screen of known kinase inhibitors against a panel of 300 human protein kinases. Biochemical and structural studies indicate that this class achieves its high selectivity by binding to the ATP-binding pocket of inactive, unphosphorylated IGF-1R/IR and stabilizing the activation loop in a native-like inactive conformation. One member of this compound family was originally reported as an inhibitor of the serine/threonine kinase ERK, a kinase that is distinct in the structure of its unphosphorylated/inactive form from IR/IGF-1R. Remarkably, this compound binds to the ATP-binding pocket of ERK in an entirely different conformation to that of IGF-1R/IR, explaining the potency against these two structurally distinct kinase families. These findings suggest a novel approach to polypharmacology in which two or more unrelated kinases are inhibited by a single compound that targets different conformations of each target kinase.
Collapse
Affiliation(s)
- Theonie Anastassiadis
- From the Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - Krisna C. Duong-Ly
- From the Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - Sean W. Deacon
- Reaction Biology Corporation, Malvern, Pennsylvania 19355
| | - Alec Lafontant
- the Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, and
| | - Haiching Ma
- Reaction Biology Corporation, Malvern, Pennsylvania 19355
| | - Karthik Devarajan
- the Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - Roland L. Dunbrack
- the Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, and
| | - Jinhua Wu
- the Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, and
| | - Jeffrey R. Peterson
- From the Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, , To whom correspondence should be addressed: Fox Chase Cancer Center, 333 Cottman Ave., Rm. P3165, Philadelphia, PA 19111. Tel.: 215-728-3568; Fax: 215-728-3574; E-mail:
| |
Collapse
|