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CDK/CK1 inhibitors roscovitine and CR8 downregulate amplified MYCN in neuroblastoma cells. Oncogene 2013; 33:5675-87. [PMID: 24317512 DOI: 10.1038/onc.2013.513] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 10/09/2013] [Accepted: 10/21/2013] [Indexed: 12/15/2022]
Abstract
To understand the mechanisms of action of (R)-roscovitine and (S)-CR8, two related pharmacological inhibitors of cyclin-dependent kinases (CDKs), we applied a variety of '-omics' techniques to the human neuroblastoma SH-SY5Y and IMR32 cell lines: (1) kinase interaction assays, (2) affinity competition on immobilized broad-spectrum kinase inhibitors, (3) affinity chromatography on immobilized (R)-roscovitine and (S)-CR8, (4) whole genome transcriptomics analysis and specific quantitative PCR studies, (5) global quantitative proteomics approach and western blot analysis of selected proteins. Altogether, the results show that the major direct targets of these two molecules belong to the CDKs (1,2,5,7,9,12), DYRKs, CLKs and CK1s families. By inhibiting CDK7, CDK9 and CDK12, these inhibitors transiently reduce RNA polymerase 2 activity, which results in downregulation of a large set of genes. Global transcriptomics and proteomics analysis converge to a central role of MYC transcription factors downregulation. Indeed, CDK inhibitors trigger rapid and massive downregulation of MYCN expression in MYCN-amplified neuroblastoma cells as well as in nude mice xenografted IMR32 cells. Inhibition of casein kinase 1 may also contribute to the antitumoral activity of (R)-roscovitine and (S)-CR8. This dual mechanism of action may be crucial in the use of these kinase inhibitors for the treatment of MYC-dependent cancers, in particular neuroblastoma where MYCN amplification is a strong predictor factor for high-risk disease.
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152
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Deau E, Loidreau Y, Marchand P, Nourrisson MR, Loaëc N, Meijer L, Levacher V, Besson T. Synthesis of novel 7-substituted pyrido[2',3':4,5]furo[3,2-d]pyrimidin-4-amines and their N-aryl analogues and evaluation of their inhibitory activity against Ser/Thr kinases. Bioorg Med Chem Lett 2013; 23:6784-8. [PMID: 24176400 DOI: 10.1016/j.bmcl.2013.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/07/2013] [Accepted: 10/08/2013] [Indexed: 10/26/2022]
Abstract
The efficient synthesis of 7-substituted pyrido[2',3':4,5]furo[3,2-d]pyrimidin-4-amines and their N-aryl analogues is described. 3,5-Dibromopyridine was converted into 3-amino-6-bromofuro[3,2-b]pyridine-2-carbonitrile intermediate which was formylated with DMFDMA. Functionalization at position 7 of the tricyclic scaffold was accomplished, before or after cyclisation step, by palladium-catalyzed Suzuki-Miyaura cross-coupling while the pyrimidin-4-amines and N-aryl counterparts were synthesized by microwave-assisted formamide degradation and Dimroth rearrangement, respectively. The final products were evaluated for their potent inhibition of a series of five Ser/Thr kinases (CDK5/p25, CK1δ/ε, CLK1, DYRK1A, GSK3α/β). Compound 35 showed the best inhibitory activity with an IC50 value of 49 nM and proved to be specific to CLK1 among the panel of tested kinases.
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Affiliation(s)
- Emmanuel Deau
- Normandie Univ, COBRA, UMR 6014 & FR 3038; Univ Rouen; INSA Rouen; CNRS, Bâtiment IRCOF, 1 rue Tesnière, 76821 Mont St Aignan Cedex, France
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153
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154
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Yoshida K, Itoyama R, Yamahira M, Tanaka J, Loaëc N, Lozach O, Durieu E, Fukuda T, Ishibashi F, Meijer L, Iwao M. Synthesis, Resolution, and Biological Evaluation of Atropisomeric (aR)- and (aS)-16-Methyllamellarins N: Unique Effects of the Axial Chirality on the Selectivity of Protein Kinases Inhibition. J Med Chem 2013; 56:7289-301. [DOI: 10.1021/jm400719y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Kenyu Yoshida
- Division
of Chemistry and Materials Sciences, Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Ryosuke Itoyama
- Division
of Chemistry and Materials Sciences, Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Masashi Yamahira
- Division
of Marine Life Science and Biochemistry, Graduate School of Fisheries
Science and Environmental Studies, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Junji Tanaka
- Institute
for Materials Chemistry and Engineering, Kyushu University, Kasuga
Koen 6-1, Kasuga 816-8580, Japan
| | - Nadège Loaëc
- Protein
Phosphorylation and Human Disease Group, Station Biologique, CNRS, 29680 Roscoff, Bretagne, France
- ManRos Therapeutics, Centre de Perharidy, 29680 Roscoff, Bretagne, France
| | - Olivier Lozach
- Protein
Phosphorylation and Human Disease Group, Station Biologique, CNRS, 29680 Roscoff, Bretagne, France
| | - Emilie Durieu
- Protein
Phosphorylation and Human Disease Group, Station Biologique, CNRS, 29680 Roscoff, Bretagne, France
- ManRos Therapeutics, Centre de Perharidy, 29680 Roscoff, Bretagne, France
| | - Tsutomu Fukuda
- Division
of Chemistry and Materials Sciences, Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Fumito Ishibashi
- Division
of Marine Life Science and Biochemistry, Graduate School of Fisheries
Science and Environmental Studies, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Laurent Meijer
- Protein
Phosphorylation and Human Disease Group, Station Biologique, CNRS, 29680 Roscoff, Bretagne, France
- ManRos Therapeutics, Centre de Perharidy, 29680 Roscoff, Bretagne, France
| | - Masatomo Iwao
- Division
of Chemistry and Materials Sciences, Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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155
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Cozza G, Sarno S, Ruzzene M, Girardi C, Orzeszko A, Kazimierczuk Z, Zagotto G, Bonaiuto E, Di Paolo ML, Pinna LA. Exploiting the repertoire of CK2 inhibitors to target DYRK and PIM kinases. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1834:1402-9. [PMID: 23360763 DOI: 10.1016/j.bbapap.2013.01.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 01/14/2013] [Accepted: 01/17/2013] [Indexed: 10/27/2022]
Abstract
Advantage has been taken of the relative promiscuity of commonly used inhibitors of protein kinase CK2 to develop compounds that can be exploited for the selective inhibition of druggable kinases other than CK2 itself. Here we summarize data obtained by altering the scaffold of CK2 inhibitors to give rise to novel selective inhibitors of DYRK1A and to a powerful cell permeable dual inhibitor of PIM1 and CK2. In the former case one of the new compounds, C624 (naphto [1,2-b]benzofuran-5,9-diol) displays a potency comparable to that of the first-in-class DYRK1A inhibitor, harmine, lacking however the drawback of drastically inhibiting monoamine oxidase-A (MAO-A) as harmine does. On the other hand the promiscuous CK2 inhibitor 4,5,6,7-tetrabromo-1H-benzimidazole (TBI,TBBz) has been derivatized with a sugar moiety to generate a 1-(β-D-2'-deoxyribofuranosyl)-4,5,6,7-tetrabromo-1H-benzimidazole (TDB) compound which inhibits PIM1 and CK2 with comparably high efficacy (IC50 values<100nM) and remarkable selectivity. TDB, unlike other dual PIM1/CK2 inhibitors described in the literature is readily cell permeable and displays a cytotoxic effect on cancer cells consistent with concomitant inhibition of both its onco-kinase targets. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
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Affiliation(s)
- Giorgio Cozza
- Department of Biomedical Sciences and CNR, Institute of Neuroscience, University of Padua, Viale G. Colombo 3 35131, Padova, Italy
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156
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Bharate SB, Sawant SD, Singh PP, Vishwakarma RA. Kinase inhibitors of marine origin. Chem Rev 2013; 113:6761-815. [PMID: 23679846 DOI: 10.1021/cr300410v] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sandip B Bharate
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine (Council of Scientific and Industrial Research), Canal Road, Jammu-180001, India
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157
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Pan Y, Wang Y, Bryant SH. Pharmacophore and 3D-QSAR characterization of 6-arylquinazolin-4-amines as Cdc2-like kinase 4 (Clk4) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) inhibitors. J Chem Inf Model 2013; 53:938-47. [PMID: 23496085 PMCID: PMC3633254 DOI: 10.1021/ci300625c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Indexed: 01/23/2023]
Abstract
Cdc2-like kinase 4 (Clk4) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) are protein kinases that are promising targets for treatment of diseases caused by abnormal gene splicing. 6-Arylquinazolin-4-amines have been recently identified as potent Clk4 and Dyrk1A inhibitors. In order to understand the structure-activity correlation of these analogs, we have applied ligand-based pharmacophore and 3D-QSAR modeling combined with structure-based homology modeling and docking. The high R(2) and Q(2) (0.88 and 0.79 for Clk4, 0.85 and 0.82 for Dyrk1A, respectively) based on validation with training and test set compounds suggested that the generated 3D-QSAR models are reliable in predicting novel ligand activities against Clk4 and Dyrk1A. The binding mode identified through docking ligands to the ATP binding domain of Clk4 was consistent with the structural properties and energy field contour maps characterized by pharmacophore and 3D-QSAR models and gave valuable insights into the structure-activity profile of 6-arylquinazolin-4-amine analogs. The obtained 3D-QSAR and pharmacophore models in combination with the binding mode between inhibitor and residues of Clk4 will be helpful for future lead compound identification and optimization to design potent and selective Clk4 and Dyrk1A inhibitors.
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Affiliation(s)
- Yongmei Pan
- National Center for
Biotechnology Information, National
Library of Medicine, National Institution of Health, 8600 Rockville
Pike, Bethesda, Maryland 20894, United States
| | - Yanli Wang
- National Center for
Biotechnology Information, National
Library of Medicine, National Institution of Health, 8600 Rockville
Pike, Bethesda, Maryland 20894, United States
| | - Stephen H. Bryant
- National Center for
Biotechnology Information, National
Library of Medicine, National Institution of Health, 8600 Rockville
Pike, Bethesda, Maryland 20894, United States
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158
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Pan Y, Wang Y, Bryant SH. Pharmacophore and 3D-QSAR characterization of 6-arylquinazolin-4-amines as Cdc2-like kinase 4 (Clk4) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) inhibitors. J Chem Inf Model 2013. [PMID: 23496085 DOI: 10.1021/ci300635c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cdc2-like kinase 4 (Clk4) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) are protein kinases that are promising targets for treatment of diseases caused by abnormal gene splicing. 6-Arylquinazolin-4-amines have been recently identified as potent Clk4 and Dyrk1A inhibitors. In order to understand the structure-activity correlation of these analogs, we have applied ligand-based pharmacophore and 3D-QSAR modeling combined with structure-based homology modeling and docking. The high R(2) and Q(2) (0.88 and 0.79 for Clk4, 0.85 and 0.82 for Dyrk1A, respectively) based on validation with training and test set compounds suggested that the generated 3D-QSAR models are reliable in predicting novel ligand activities against Clk4 and Dyrk1A. The binding mode identified through docking ligands to the ATP binding domain of Clk4 was consistent with the structural properties and energy field contour maps characterized by pharmacophore and 3D-QSAR models and gave valuable insights into the structure-activity profile of 6-arylquinazolin-4-amine analogs. The obtained 3D-QSAR and pharmacophore models in combination with the binding mode between inhibitor and residues of Clk4 will be helpful for future lead compound identification and optimization to design potent and selective Clk4 and Dyrk1A inhibitors.
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Affiliation(s)
- Yongmei Pan
- National Center for Biotechnology Information, National Library of Medicine, National Institution of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
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159
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Burgy G, Tahtouh T, Durieu E, Foll-Josselin B, Limanton E, Meijer L, Carreaux F, Bazureau JP. Chemical synthesis and biological validation of immobilized protein kinase inhibitory Leucettines. Eur J Med Chem 2013; 62:728-37. [DOI: 10.1016/j.ejmech.2013.01.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/25/2013] [Accepted: 01/29/2013] [Indexed: 12/30/2022]
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160
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Loidreau Y, Marchand P, Dubouilh-Benard C, Nourrisson MR, Duflos M, Loaëc N, Meijer L, Besson T. Synthesis and biological evaluation of N-aryl-7-methoxybenzo[b]furo[3,2-d]pyrimidin-4-amines and their N-arylbenzo[b]thieno[3,2-d]pyrimidin-4-amine analogues as dual inhibitors of CLK1 and DYRK1A kinases. Eur J Med Chem 2013; 59:283-95. [PMID: 23237976 DOI: 10.1016/j.ejmech.2012.11.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 11/12/2012] [Accepted: 11/19/2012] [Indexed: 01/04/2023]
Abstract
Novel N-aryl-7-methoxybenzo[b]furo[3,2-d]pyrimidin-4-amines (1) and their N-arylbenzo[b]thieno[3,2-d]pyrimidin-4-amine analogues (2) were designed and prepared for the first time via microwave-accelerated multi-step synthesis. Various anilines were condensed with N'-(2-cyanaryl)-N,N-dimethylformimidamide intermediates obtained by reaction of 3-amino-6-methoxybenzofuran-2-carbonitrile (3) and 3-amino-6-methoxybenzothiophene-2-carbonitrile (4) precursors with dimethylformamide dimethylacetal. The inhibitory potency of the final products against five protein kinases (CDK5/p25, CK1δ/ε, GSK3α/β, DYRK1A and CLK1) was estimated. Compounds (2a-z) turned out to be particularly promising for the development of new pharmacological dual inhibitors of CLK1 and DYRK1A kinases.
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Affiliation(s)
- Yvonnick Loidreau
- Université de Rouen, Laboratoire de Chimie Organique et Bio-organique, Réactivité et Analyse (C.O.B.R.A.), CNRS UMR 6014 & FR3038, Institut de Recherche en Chimie Organique Fine (I.R.C.O.F.) rue Tesnière, 76130 Mont Saint-Aignan, France
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