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Zheng J, Yates SP, Jia Z. Structural and mechanistic insights into the bifunctional enzyme isocitrate dehydrogenase kinase/phosphatase AceK. Philos Trans R Soc Lond B Biol Sci 2012; 367:2656-68. [PMID: 22889914 DOI: 10.1098/rstb.2011.0426] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The switch between the Krebs cycle and the glyoxylate bypass is controlled by isocitrate dehydrogenase kinase/phosphatase (AceK). AceK, a bifunctional enzyme, phosphorylates and dephosphorylates isocitrate dehydrogenase (IDH) with its unique active site that harbours both the kinase and ATP/ADP-dependent phosphatase activities. AceK was the first example of prokaryotic phosphorylation identified, and the recent characterization of the structures of AceK and its complex with its protein substrate, IDH, now offers a new understanding of both previous and future endeavours. AceK is structurally similar to the eukaryotic protein kinase superfamily, sharing many of the familiar catalytic and regulatory motifs, demonstrating a close evolutionary relationship. Although the active site is shared by both the kinase and phosphatase functions, the catalytic residues needed for phosphatase function are readily seen when compared with the DXDX(T/V) family of phosphatases, despite the fact that the phosphatase function of AceK is strictly ATP/ADP-dependent. Structural analysis has also allowed a detailed look at regulation and its stringent requirements for interacting with IDH.
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Affiliation(s)
- Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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52
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Natural-product-derived fragments for fragment-based ligand discovery. Nat Chem 2012; 5:21-8. [DOI: 10.1038/nchem.1506] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 10/19/2012] [Indexed: 12/11/2022]
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53
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Grütter C, Simard JR, Mayer-Wrangowski SC, Schreier PH, Pérez-Martín J, Richters A, Getlik M, Gutbrod O, Braun CA, Beck ME, Rauh D. Targeting GSK3 from Ustilago maydis: type-II kinase inhibitors as potential antifungals. ACS Chem Biol 2012; 7:1257-67. [PMID: 22545924 DOI: 10.1021/cb300128b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein kinases are key enzymes in the complex regulation of cellular processes in almost all living organisms. For this reason, protein kinases represent attractive targets to stop the growth of eukaryotic pathogens such as protozoa and fungi. However, using kinase inhibitors to fight against these organisms bears several challenges since most of them are unselective and will also affect crucial host kinases. Here we present the X-ray structure of glycogen synthase kinase 3 from the fungal plant pathogen Ustilago maydis (UmGSK3) and its inhibition by type-II kinase inhibitors. Despite the high sequence homology between the human and the fungal variant of this vital kinase, we found substantial differences in the conformational plasticity of their active sites. Compounds that induced such conformational changes could be used to selectively inhibit the fungal kinase. This study serves as an example of how species-specific selectivity of inhibitors can be achieved by identifying and addressing the inactive state of a protein kinase. In addition to this, our study gives interesting insights into the molecular plasticity of UmGSK3 by revealing a previously unknown inactive conformation of this important kinase family.
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Affiliation(s)
- Christian Grütter
- Fakultät
Chemie - Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse
15, D-44227 Dortmund, Germany
| | - Svenja C. Mayer-Wrangowski
- Fakultät
Chemie - Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Peter H. Schreier
- Bayer CropScience AG, Alfred-Nobel-Strasse 50, D-40789 Monheim
am Rhein, Germany
- Institute
for Genetics, University of Cologne, Zülpicher
Strasse 47a, D-50674 Cologne, Germany
| | - José Pérez-Martín
- Institute of Functional Biology and Genomics, CSIC, 37007 Salamanca, Spain
| | - André Richters
- Fakultät
Chemie - Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse
15, D-44227 Dortmund, Germany
| | - Matthäus Getlik
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse
15, D-44227 Dortmund, Germany
| | - Oliver Gutbrod
- Bayer CropScience AG, Alfred-Nobel-Strasse 50, D-40789 Monheim
am Rhein, Germany
| | - Christoph A. Braun
- Bayer CropScience AG, Alfred-Nobel-Strasse 50, D-40789 Monheim
am Rhein, Germany
| | - Michael E. Beck
- Bayer CropScience AG, Alfred-Nobel-Strasse 50, D-40789 Monheim
am Rhein, Germany
| | - Daniel Rauh
- Fakultät
Chemie - Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse
15, D-44227 Dortmund, Germany
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54
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Getlik M, Simard JR, Termathe M, Grütter C, Rabiller M, van Otterlo WAL, Rauh D. Fluorophore labeled kinase detects ligands that bind within the MAPK insert of p38α kinase. PLoS One 2012; 7:e39713. [PMID: 22768308 PMCID: PMC3388095 DOI: 10.1371/journal.pone.0039713] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 05/25/2012] [Indexed: 11/19/2022] Open
Abstract
The vast majority of small molecules known to modulate kinase activity, target the highly conserved ATP-pocket. Consequently, such ligands are often less specific and in case of inhibitors, this leads to the inhibition of multiple kinases. Thus, selective modulation of kinase function remains a major hurdle. One of the next great challenges in kinase research is the identification of ligands which bind to less conserved sites and target the non-catalytic functions of protein kinases. However, approaches that allow for the unambiguous identification of molecules that bind to these less conserved sites are few in number. We have previously reported the use of fluorescent labels in kinases (FLiK) to develop direct kinase binding assays that exclusively detect ligands which stabilize inactive (DFG-out) kinase conformations. Here, we present the successful application of the FLiK approach to develop a high-throughput binding assay capable of directly monitoring ligand binding to a remote site within the MAPK insert of p38α mitogen-activated protein kinase (MAPK). Guided by the crystal structure of an initially identified hit molecule in complex with p38α, we developed a tight binding ligand which may serve as an ideal starting point for further investigations of the biological function of the MAPK insert in regulating the p38α signaling pathway.
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Affiliation(s)
- Matthäus Getlik
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Martin Termathe
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Christian Grütter
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Fakultät Chemie, Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias Rabiller
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Willem A. L. van Otterlo
- Department of Chemistry and Polymer Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Daniel Rauh
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Fakultät Chemie, Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
- * E-mail:
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55
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Milletti F, Hermann JC. Targeted kinase selectivity from kinase profiling data. ACS Med Chem Lett 2012; 3:383-6. [PMID: 24900482 DOI: 10.1021/ml300012r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 03/14/2012] [Indexed: 01/17/2023] Open
Abstract
Kinase selectivity plays a major role in the design strategy of lead series and in the ultimate success of kinase drug discovery programs. Although profiling compounds against a large panel of protein kinases has become a standard part of modern drug discovery, data accumulated from these kinase panels may be underutilized for new kinase projects. We present a method that can be used to optimize the selectivity profile of a compound using historical kinase profiling data. This method proposes chemical transformations based on pairs of very similar compounds, which are both active against a desired target kinase and differ in activity against another kinase. We show that these transformations are transferable across scaffolds, thus making this tool valuable to exploit kinase profiling data for unrelated series of compounds.
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Affiliation(s)
- Francesca Milletti
- pRED Informatics, Roche, 340 Kingsland Street, Nutley, New Jersey 07110,
United States
| | - Johannes C. Hermann
- Discovery
Chemistry, Roche, 340 Kingsland Street,
Nutley, New Jersey 07110, United States
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56
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Koch A, Rode HB, Richters A, Rauh D, Hauf S. A chemical genetic approach for covalent inhibition of analogue-sensitive aurora kinase. ACS Chem Biol 2012; 7:723-31. [PMID: 22264160 DOI: 10.1021/cb200465c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The perturbation of protein kinases with small organic molecules is a powerful approach to dissect kinase function in complex biological systems. Covalent kinase inhibitors that target thiols in the ATP binding pocket of the kinase domain proved to be ideal reagents for the investigation of highly dynamic cellular processes. However, due to the covalent inhibitors' possible off-target reactivities, it is required that the overall shape of the inhibitor as well as the intrinsic reactivity of the electrophile are precisely tuned to favor the reaction with only the desired cysteine. Here we report on the design and biological characterization of covalent anilinoquinazolines as potent inhibitors of genetically engineered Aurora kinase in fission yeast.
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Affiliation(s)
- André Koch
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse
39, D-72076 Tübingen, Germany
| | - Haridas B. Rode
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse
15, D-44227 Dortmund, Germany
- Council of Scientific and Industrial Research (CSIR) Headquarters, 2, Rafi
Marg, New Delhi-110001, India
| | - André Richters
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse
15, D-44227 Dortmund, Germany
| | - Daniel Rauh
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse
15, D-44227 Dortmund, Germany
- Fakultät Chemie, Chemische
Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Silke Hauf
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse
39, D-72076 Tübingen, Germany
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57
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Structure-based design, synthesis and biological evaluation of N-pyrazole, N′-thiazole urea inhibitors of MAP kinase p38α. Eur J Med Chem 2012; 48:1-15. [DOI: 10.1016/j.ejmech.2011.11.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 11/05/2011] [Accepted: 11/09/2011] [Indexed: 11/22/2022]
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58
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Simard JR, Rauh D. Fluorescence labels in kinases: a high-throughput kinase binding assay for the identification of DFG-out binding ligands. Methods Mol Biol 2012; 800:95-117. [PMID: 21964785 DOI: 10.1007/978-1-61779-349-3_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Despite the hundreds of kinase inhibitors currently in discovery and pre-clinical phases, the number of kinase inhibitors which have been approved and are on the market remains low by comparison. This discrepancy reflects the challenges which accompany the development of kinase inhibitors which are relatively specific and less toxic. Targeting protein kinases with ATP-competitive inhibitors has been the classical approach to inhibiting kinase activity, but the highly conserved nature of the ATP-binding site contributes to poor inhibitor selectivity, issues which have particularly hampered the development of novel kinase inhibitors. We developed a high-throughput screening technology that can discriminate for inhibitors which stabilize the inactive "DFG-out" kinase conformation by binding within an allosteric pocket adjacent to the ATP-binding site. Here, we describe how to use this approach to measure the K (d) of ligands, as well as how to kinetically characterize the binding and dissociation of ligands to the kinase. We also describe how this technology can be used to rapidly screen small molecule libraries at high throughput.
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Affiliation(s)
- Jeffrey R Simard
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
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59
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Nirschl M, Ottl J, Vörös J. Conformational Changes of Calmodulin on Calcium and Peptide Binding Monitored by Film Bulk Acoustic Resonators. BIOSENSORS 2011; 1:164-76. [PMID: 25585566 PMCID: PMC4264349 DOI: 10.3390/bios1040164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/04/2011] [Accepted: 12/12/2011] [Indexed: 11/21/2022]
Abstract
Film bulk acoustic resonators (FBAR) are mass sensitive, label-free biosensors that allow monitoring of the interaction between biomolecules. In this paper we use the FBAR to measure the binding of calcium and the CaMKII peptide to calmodulin. Because the mass of the calcium is too small to be detected, the conformational change caused by the binding process is measured by monitoring the resonant frequency and the motional resistance of the FBAR. The resonant frequency is a measure for the amount of mass coupled to the sensor while the motional resistance is influenced by the viscoelastic properties of the adsorbent. The measured frequency shift during the calcium adsorptions was found to be strongly dependent on the surface concentration of the immobilized calmodulin, which indicates that the measured signal is significantly influenced by the amount of water inside the calmodulin layer. By plotting the measured motional resistance against the frequency shift, a mass adsorption can be distinguished from processes involving measurable conformational changes. With this method three serial processes were identified during the peptide binding. The results show that the FBAR is a promising technology for the label-free measurement of conformational changes.
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Affiliation(s)
- Martin Nirschl
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich Gloriastrasse 35, 8092 Zurich, Switzerland.
| | - Johannes Ottl
- Novartis Institute of Biomedical Research Basel, CPC/LFP, Novartis Pharma AG, Postfach, Basel CH 4002, Switzerland.
| | - Janos Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich Gloriastrasse 35, 8092 Zurich, Switzerland.
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60
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Structural basis for basal activity and autoactivation of abscisic acid (ABA) signaling SnRK2 kinases. Proc Natl Acad Sci U S A 2011; 108:21259-64. [PMID: 22160701 DOI: 10.1073/pnas.1118651109] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Abscisic acid (ABA) is an essential hormone that controls plant growth, development, and responses to abiotic stresses. Central for ABA signaling is the ABA-mediated autoactivation of three monomeric Snf1-related kinases (SnRK2.2, -2.3, and -2.6). In the absence of ABA, SnRK2s are kept in an inactive state by forming physical complexes with type 2C protein phosphatases (PP2Cs). Upon relief of this inhibition, SnRK2 kinases can autoactivate through unknown mechanisms. Here, we report the crystal structures of full-length Arabidopsis thaliana SnRK2.3 and SnRK2.6 at 1.9- and 2.3-Å resolution, respectively. The structures, in combination with biochemical studies, reveal a two-step mechanism of intramolecular kinase activation that resembles the intermolecular activation of cyclin-dependent kinases. First, release of inhibition by PP2C allows the SnRK2s to become partially active because of an intramolecular stabilization of the catalytic domain by a conserved helix in the kinase regulatory domain. This stabilization enables SnRK2s to gain full activity by activation loop autophosphorylation. Autophosphorylation is more efficient in SnRK2.6, which has higher stability than SnRK2.3 and has well-structured activation loop phosphate acceptor sites that are positioned next to the catalytic site. Together, these data provide a structural framework that links ABA-mediated release of PP2C inhibition to activation of SnRK2 kinases.
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61
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van Beuge MM, Poelstra K, Prakash J. Specific delivery of kinase inhibitors in nonmalignant and malignant diseases. Expert Opin Drug Deliv 2011; 9:59-70. [PMID: 22111941 DOI: 10.1517/17425247.2012.638625] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Kinase inhibitors have been hailed as a breakthrough in the treatment of cancer. Extensive research is now being devoted to the development of kinase inhibitors as a treatment for many nonmalignant diseases. However, the use of kinase inhibitors in both malignant and nonmalignant diseases is also associated with side effects and the development of resistance. It may be worthwhile to explore whether cell-specific delivery of kinase inhibitors improves therapeutic efficacy and reduces side effects. AREAS COVERED This review aims to provide an overview of the preclinical studies performed to examine the specific targeting of kinase inhibitors in vitro and in vivo. It gives an introduction to kinase signaling pathways induced during disease, along with the possible problems associated with their inhibition. It also discusses the studies on specific delivery and shows that altering the specificity of kinase inhibitors by targeting methods improves their effectivity and safety. EXPERT OPINION Compared with the delivery of cytotoxic compounds, the specific delivery of kinase inhibitors has not yet been studied extensively. The studies discussed in this review provide an insight into methods used to target kinase inhibitors to different organs. The targeting of different kinase inhibitors has improved their therapeutic possibilities, but many questions still remain to be studied.
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Affiliation(s)
- Marike Marjolijn van Beuge
- University of Groningen, University Centre for Pharmacy, Department of Pharmacokinetics, Toxicology & Targeting, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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62
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Seaton DD, Krishnan J. The coupling of pathways and processes through shared components. BMC SYSTEMS BIOLOGY 2011; 5:103. [PMID: 21714894 PMCID: PMC3162518 DOI: 10.1186/1752-0509-5-103] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 06/29/2011] [Indexed: 02/08/2023]
Abstract
Background The coupling of pathways and processes through shared components is being increasingly recognised as a common theme which occurs in many cell signalling contexts, in which it plays highly non-trivial roles. Results In this paper we develop a basic modelling and systems framework in a general setting for understanding the coupling of processes and pathways through shared components. Our modelling framework starts with the interaction of two components with a common third component and includes production and degradation of all these components. We analyze the signal processing in our model to elucidate different aspects of the coupling. We show how different kinds of responses, including "ultrasensitive" and adaptive responses, may occur in this setting. We then build on the basic model structure and examine the effects of additional control regulation, switch-like signal processing, and spatial signalling. In the process, we identify a way in which allosteric regulation may contribute to signalling specificity, and how competitive effects may allow an enzyme to robustly coordinate and time the activation of parallel pathways. Conclusions We have developed and analyzed a common systems platform for examining the effects of coupling of processes through shared components. This can be the basis for subsequent expansion and understanding the many biologically observed variations on this common theme.
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Affiliation(s)
- Daniel D Seaton
- Dept. of Chemical Engineering and Centre for Process Systems Engineering Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
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63
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Thal DM, Yeow RY, Schoenau C, Huber J, Tesmer JJG. Molecular mechanism of selectivity among G protein-coupled receptor kinase 2 inhibitors. Mol Pharmacol 2011; 80:294-303. [PMID: 21596927 DOI: 10.1124/mol.111.071522] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are key regulators of cell physiology and control processes ranging from glucose homeostasis to contractility of the heart. A major mechanism for the desensitization of activated GPCRs is their phosphorylation by GPCR kinases (GRKs). Overexpression of GRK2 is strongly linked to heart failure, and GRK2 has long been considered a pharmaceutical target for the treatment of cardiovascular disease. Several lead compounds developed by Takeda Pharmaceuticals show high selectivity for GRK2 and therapeutic potential for the treatment of heart failure. To understand how these drugs achieve their selectivity, we determined crystal structures of the bovine GRK2-Gβγ complex in the presence of two of these inhibitors. Comparison with the apoGRK2-Gβγ structure demonstrates that the compounds bind in the kinase active site in a manner similar to that of the AGC kinase inhibitor balanol. Both balanol and the Takeda compounds induce a slight closure of the kinase domain, the degree of which correlates with the potencies of the inhibitors. Based on our crystal structures and homology modeling, we identified five amino acids surrounding the inhibitor binding site that we hypothesized could contribute to inhibitor selectivity. However, our results indicate that these residues are not major determinants of selectivity among GRK subfamilies. Rather, selectivity is achieved by the stabilization of a unique inactive conformation of the GRK2 kinase domain.
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Affiliation(s)
- David M Thal
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Room 3425, Ann Arbor, MI 48109, USA.
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64
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Using small molecules to target protein phosphatases. Bioorg Med Chem 2011; 19:2145-55. [DOI: 10.1016/j.bmc.2011.02.047] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/21/2011] [Accepted: 02/23/2011] [Indexed: 11/21/2022]
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65
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Gautel M. Cytoskeletal protein kinases: titin and its relations in mechanosensing. Pflugers Arch 2011; 462:119-34. [PMID: 21416260 PMCID: PMC3114093 DOI: 10.1007/s00424-011-0946-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 02/15/2011] [Accepted: 02/18/2011] [Indexed: 12/22/2022]
Abstract
Titin, the giant elastic ruler protein of striated muscle sarcomeres, contains a catalytic kinase domain related to a family of intrasterically regulated protein kinases. The most extensively studied member of this branch of the human kinome is the Ca2+–calmodulin (CaM)-regulated myosin light-chain kinases (MLCK). However, not all kinases of the MLCK branch are functional MLCKs, and about half lack a CaM binding site in their C-terminal autoinhibitory tail (AI). A unifying feature is their association with the cytoskeleton, mostly via actin and myosin filaments. Titin kinase, similar to its invertebrate analogue twitchin kinase and likely other “MLCKs”, is not Ca2+–calmodulin-activated. Recently, local protein unfolding of the C-terminal AI has emerged as a common mechanism in the activation of CaM kinases. Single-molecule data suggested that opening of the TK active site could also be achieved by mechanical unfolding of the AI. Mechanical modulation of catalytic activity might thus allow cytoskeletal signalling proteins to act as mechanosensors, creating feedback mechanisms between cytoskeletal tension and tension generation or cellular remodelling. Similar to other MLCK-like kinases like DRAK2 and DAPK1, TK is linked to protein turnover regulation via the autophagy/lysosomal system, suggesting the MLCK-like kinases have common functions beyond contraction regulation.
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Affiliation(s)
- Mathias Gautel
- King's College London BHF Centre of Research Excellence, Cardiovascular Division, London, SE1 1UL, UK.
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66
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Sala E, Guasch L, Iwaszkiewicz J, Mulero M, Salvadó MJ, Pinent M, Zoete V, Grosdidier A, Garcia-Vallvé S, Michielin O, Pujadas G. Identification of human IKK-2 inhibitors of natural origin (part I): modeling of the IKK-2 kinase domain, virtual screening and activity assays. PLoS One 2011; 6:e16903. [PMID: 21390216 PMCID: PMC3044726 DOI: 10.1371/journal.pone.0016903] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 01/14/2011] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Their large scaffold diversity and properties, such as structural complexity and drug similarity, form the basis of claims that natural products are ideal starting points for drug design and development. Consequently, there has been great interest in determining whether such molecules show biological activity toward protein targets of pharmacological relevance. One target of particular interest is hIKK-2, a serine-threonine protein kinase belonging to the IKK complex that is the primary component responsible for activating NF-κB in response to various inflammatory stimuli. Indeed, this has led to the development of synthetic ATP-competitive inhibitors for hIKK-2. Therefore, the main goals of this study were (a) to use virtual screening to identify potential hIKK-2 inhibitors of natural origin that compete with ATP and (b) to evaluate the reliability of our virtual-screening protocol by experimentally testing the in vitro activity of selected natural-product hits. METHODOLOGY/PRINCIPAL FINDINGS We thus predicted that 1,061 out of the 89,425 natural products present in the studied database would inhibit hIKK-2 with good ADMET properties. Notably, when these 1,061 molecules were merged with the 98 synthetic hIKK-2 inhibitors used in this study and the resulting set was classified into ten clusters according to chemical similarity, there were three clusters that contained only natural products. Five molecules from these three clusters (for which no anti-inflammatory activity has been previously described) were then selected for in vitro activity testing, in which three out of the five molecules were shown to inhibit hIKK-2. CONCLUSIONS/SIGNIFICANCE We demonstrated that our virtual-screening protocol was successful in identifying lead compounds for developing new inhibitors for hIKK-2, a target of great interest in medicinal chemistry. Additionally, all the tools developed during the current study (i.e., the homology model for the hIKK-2 kinase domain and the pharmacophore) will be made available to interested readers upon request.
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Affiliation(s)
- Esther Sala
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
| | - Laura Guasch
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Quartier UNIL-Sorge, Lausanne, Switzerland
| | - Miquel Mulero
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
| | - Maria-Josepa Salvadó
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
| | - Montserrat Pinent
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Quartier UNIL-Sorge, Lausanne, Switzerland
| | - Aurélien Grosdidier
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Quartier UNIL-Sorge, Lausanne, Switzerland
| | - Santiago Garcia-Vallvé
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
- Centre Tecnològic de Nutrició i Salut, Reus, Catalonia, Spain
| | - Olivier Michielin
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Quartier UNIL-Sorge, Lausanne, Switzerland
| | - Gerard Pujadas
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
- Centre Tecnològic de Nutrició i Salut, Reus, Catalonia, Spain
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Klüter S, Simard JR, Rode HB, Grütter C, Pawar V, Raaijmakers HCA, Barf TA, Rabiller M, van Otterlo WAL, Rauh D. Characterization of Irreversible Kinase Inhibitors by Directly Detecting Covalent Bond Formation: A Tool for Dissecting Kinase Drug Resistance. Chembiochem 2010; 11:2557-66. [DOI: 10.1002/cbic.201000352] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Rode HB, Sos ML, Grütter C, Heynck S, Simard JR, Rauh D. Synthesis and biological evaluation of 7-substituted-1-(3-bromophenylamino)isoquinoline-4-carbonitriles as inhibitors of myosin light chain kinase and epidermal growth factor receptor. Bioorg Med Chem 2010; 19:429-39. [PMID: 21130659 DOI: 10.1016/j.bmc.2010.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 11/02/2010] [Accepted: 11/04/2010] [Indexed: 12/22/2022]
Abstract
Here we present the synthesis and biological activity of a series of 7-substituted-1-(3-bromophenylamino)isoquinoline-4-carbonitriles as inhibitors of myosin light chain kinase (MLCK) and the epidermal growth factor receptor kinase (EGFR). The inhibitory effect of these molecules was found to be dependent on the nature of the substituents at the 7-position of the isoquinoline scaffold.
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Affiliation(s)
- Haridas B Rode
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany
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Cheng S, Niv MY. Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation. J Chem Inf Model 2010; 50:1602-10. [DOI: 10.1021/ci100076j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shu Cheng
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University, Rehovot 76100, Israel
| | - Masha Y. Niv
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University, Rehovot 76100, Israel
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Robubi A, Waldmann H, Rauh D. RAF Kinase Inhibitors in Cancer Treatment: Like a Bull in a China Shop? Chembiochem 2010; 11:1645-8. [DOI: 10.1002/cbic.201000348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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