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Perdoux R, Barrada A, Boulaiz M, Garau C, Belbachir C, Lecampion C, Montané MH, Menand B. A drug-resistant mutation in plant target of rapamycin validates the specificity of ATP-competitive TOR inhibitors in vivo. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1344-1355. [PMID: 38011587 DOI: 10.1111/tpj.16564] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Kinases are major components of cellular signaling pathways, regulating key cellular activities through phosphorylation. Kinase inhibitors are efficient tools for studying kinase targets and functions, however assessing their kinase specificity in vivo is essential. The identification of resistant kinase mutants has been proposed to be the most convincing approach to achieve this goal. Here, we address this issue in plants via a pharmacogenetic screen for mutants resistant to the ATP-competitive TOR inhibitor AZD-8055. The eukaryotic TOR (Target of Rapamycin) kinase is emerging as a major hub controlling growth responses in plants largely thanks to the use of ATP-competitive inhibitors. We identified a dominant mutation in the DFG motif of the Arabidopsis TOR kinase domain that leads to very strong resistance to AZD-8055. This resistance was characterized by measuring root growth, photosystem II (PSII) activity in leaves and phosphorylation of YAK1 (Yet Another Kinase 1) and RPS6 (Ribosomal protein S6), a direct and an indirect target of TOR respectively. Using other ATP-competitive TOR inhibitors, we also show that the dominant mutation is particularly efficient for resistance to drugs structurally related to AZD-8055. Altogether, this proof-of-concept study demonstrates that a pharmacogenetic screen in Arabidopsis can be used to successfully identify the target of a kinase inhibitor in vivo and therefore to demonstrate inhibitor specificity. Thanks to the conservation of kinase families in eukaryotes, and the possibility of creating amino acid substitutions by genome editing, this work has great potential for extending studies on the evolution of signaling pathways in eukaryotes.
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Affiliation(s)
- Romain Perdoux
- Aix-Marseille Univ, CEA, CNRS, BIAM, LGBP Team, Marseille, France
| | - Adam Barrada
- Aix-Marseille Univ, CEA, CNRS, BIAM, LGBP Team, Marseille, France
| | - Manal Boulaiz
- Aix-Marseille Univ, CEA, CNRS, BIAM, LGBP Team, Marseille, France
| | - Camille Garau
- Aix-Marseille Univ, CEA, CNRS, BIAM, LGBP Team, Marseille, France
| | | | - Cécile Lecampion
- Aix-Marseille Univ, CEA, CNRS, BIAM, LGBP Team, Marseille, France
| | | | - Benoît Menand
- Aix-Marseille Univ, CEA, CNRS, BIAM, LGBP Team, Marseille, France
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2
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Targeting Human Proteins for Antiviral Drug Discovery and Repurposing Efforts: A Focus on Protein Kinases. Viruses 2023; 15:v15020568. [PMID: 36851782 PMCID: PMC9966946 DOI: 10.3390/v15020568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Despite the great technological and medical advances in fighting viral diseases, new therapies for most of them are still lacking, and existing antivirals suffer from major limitations regarding drug resistance and a limited spectrum of activity. In fact, most approved antivirals are directly acting antiviral (DAA) drugs, which interfere with viral proteins and confer great selectivity towards their viral targets but suffer from resistance and limited spectrum. Nowadays, host-targeted antivirals (HTAs) are on the rise, in the drug discovery and development pipelines, in academia and in the pharmaceutical industry. These drugs target host proteins involved in the virus life cycle and are considered promising alternatives to DAAs due to their broader spectrum and lower potential for resistance. Herein, we discuss an important class of HTAs that modulate signal transduction pathways by targeting host kinases. Kinases are considered key enzymes that control virus-host interactions. We also provide a synopsis of the antiviral drug discovery and development pipeline detailing antiviral kinase targets, drug types, therapeutic classes for repurposed drugs, and top developing organizations. Furthermore, we detail the drug design and repurposing considerations, as well as the limitations and challenges, for kinase-targeted antivirals, including the choice of the binding sites, physicochemical properties, and drug combinations.
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3
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Aly RM, Serya RAT, El-Motwally AM, Esmat A, Abbas S, Abou El Ella DA. Novel quinoline-3-carboxamides (Part 2): Design, optimization and synthesis of quinoline based scaffold as EGFR inhibitors with potent anticancer activity. Bioorg Chem 2017; 75:368-392. [PMID: 29096097 DOI: 10.1016/j.bioorg.2017.10.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/21/2017] [Accepted: 10/24/2017] [Indexed: 10/18/2022]
Abstract
EGFR has a key role in cell growth. Its mutation and overexpression share in epithelial malignancies and tumor growth. Quinazoline and quinoline derivatives are common anticancer intracellular inhibitors of EGFR kinase, and their optimization is an important issue for development of potent targeted anticancer agents. Based on these facts, different strategies were used for optimizing our reported quinoline-3-carboxamide compound III (EGFR IC50 = 5.283 µM and MCF-7 IC50 = 3.46 µM) through different molecular modeling techniques. The optimized compounds were synthesized and subjected to EGFR binding assay and accordingly some more potent inhibitors were obtained. The most potent quinoline-3-carboxamides were the furan derivative 5o; thiophene derivative 6b; and benzyloxy derivative 10 showing EGFR IC50 values 2.61, 0.49 and 1.73 μM, respectively. Furthermore, the anticancer activity of compounds eliciting potent EGFR inhibition (5o, 5p, 6b, 8a, 8b, and 10) was evaluated against MCF-7 cell line where they exhibited IC50 values 3.355, 3.647, 5.069, 3.617, 0.839 and 10.85 μM, respectively. Compound 6b was selected as lead structure for further optimization hoping to produce more potent EGFR inhibitors.
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Affiliation(s)
- Rasha M Aly
- National Organization for Drug Control and Research, Cairo, Egypt.
| | - Rabah A T Serya
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, ElKhalifa El Maamoon St., 11566 Abbasseya, Cairo, Egypt
| | | | - Ahmed Esmat
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, 21589 Jeddah, Saudi Arabia; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, ElKhalifa El Maamoon St., 11566 Abbasseya, Cairo, Egypt
| | - Safinaz Abbas
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt
| | - Dalal A Abou El Ella
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, ElKhalifa El Maamoon St., 11566 Abbasseya, Cairo, Egypt; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Nahda University, Nahda University Road, New Beni Suef City 72427, Egypt
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4
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Cai X, Xu Y, Cheung AK, Tomlinson RC, Alcázar-Román A, Murphy L, Billich A, Zhang B, Feng Y, Klumpp M, Rondeau JM, Fazal AN, Wilson CJ, Myer V, Joberty G, Bouwmeester T, Labow MA, Finan PM, Porter JA, Ploegh HL, Baird D, De Camilli P, Tallarico JA, Huang Q. PIKfyve, a class III PI kinase, is the target of the small molecular IL-12/IL-23 inhibitor apilimod and a player in Toll-like receptor signaling. ACTA ACUST UNITED AC 2014; 20:912-21. [PMID: 23890009 DOI: 10.1016/j.chembiol.2013.05.010] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/16/2013] [Accepted: 05/29/2013] [Indexed: 12/15/2022]
Abstract
Toll-like receptor (TLR) signaling is a key component of innate immunity. Aberrant TLR activation leads to immune disorders via dysregulation of cytokine production, such as IL-12/IL-23. Herein, we identify and characterize PIKfyve, a lipid kinase, as a critical player in TLR signaling using apilimod as an affinity tool. Apilimod is a potent small molecular inhibitor of IL-12/IL-23 with an unknown target and has been evaluated in clinical trials for patients with Crohn's disease or rheumatoid arthritis. Using a chemical genetic approach, we show that it binds to PIKfyve and blocks its phosphotransferase activity, leading to selective inhibition of IL-12/IL-23p40. Pharmacological or genetic inactivation of PIKfyve is necessary and sufficient for suppression of IL-12/IL-23p40 expression. Thus, we have uncovered a phosphoinositide-mediated regulatory mechanism that controls TLR signaling.
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Affiliation(s)
- Xinming Cai
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
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5
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Montané MH, Menand B. ATP-competitive mTOR kinase inhibitors delay plant growth by triggering early differentiation of meristematic cells but no developmental patterning change. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4361-74. [PMID: 23963679 PMCID: PMC3808319 DOI: 10.1093/jxb/ert242] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The TOR (target of rapamycin) protein, a large phosphatidylinositol 3-kinase-like protein kinase (PIKK) that is conserved in eukaryotes and is a central regulator of growth and metabolism. The analysis of function of TOR in plant growth and development has been limited by the fact that plants are very poorly sensitive to rapamycin. As the kinase domain of TOR is highly conserved, this study analysed the dose-dependent effect of three sets of first- and second-generation ATP-competitive inhibitors (called asTORis for active-site TOR inhibitors) recently developed for the human TOR kinase on Arabidopsis thaliana growth. All six asTORis inhibited plant root growth in a dose-dependent manner, with 50% growth inhibitory doses (GI50) of <10 μM and <1 μM for the first- and second-generation inhibitors, respectively, similarly to the values in mammalian cells. A genetic approach further demonstrated that only asTORis inhibited root growth in an AtTOR gene-dosage-dependent manner. AsTORis decreased the length of: (i) the meristematic zone (MZ); (ii) the division zone in the MZ; (iii) epidermal cells in the elongation zone; and (iv) root hair cells. Whereas meristematic cells committed to early differentiation, the pattern of cell differentiation was not affected per se. AsTORis-induced root hair growth phenotype was shown to be specific by using other growth inhibitors blocking the cell cycle or translation. AsTORis dose-dependent inhibition of growth and root hairs was also observed in diverse groups of flowering plants, indicating that asTORis can be used to study the TOR pathway in other angiosperms, including crop plants.
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Affiliation(s)
- Marie-Hélène Montané
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, F-13009, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales, Marseille, F-13009, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et Biotechnologie, Marseille, F-13009, France
| | - Benoît Menand
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, F-13009, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales, Marseille, F-13009, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et Biotechnologie, Marseille, F-13009, France
- * To whom correspondence should be addressed.
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Ellwood-Yen K, Keilhack H, Kunii K, Dolinski B, Connor Y, Hu K, Nagashima K, O'Hare E, Erkul Y, Di Bacco A, Gargano D, Shomer NH, Angagaw M, Leccese E, Andrade P, Hurd M, Shin MK, Vogt TF, Northrup A, Bobkova EV, Kasibhatla S, Bronson RT, Scott ML, Draetta G, Richon V, Kohl N, Blume-Jensen P, Andersen JN, Kraus M. PDK1 attenuation fails to prevent tumor formation in PTEN-deficient transgenic mouse models. Cancer Res 2011; 71:3052-65. [PMID: 21493594 DOI: 10.1158/0008-5472.can-10-2282] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PDK1 activates AKT suggesting that PDK1 inhibition might suppress tumor development. However, while PDK1 has been investigated intensively as an oncology target, selective inhibitors suitable for in vivo studies have remained elusive. In this study we present the results of in vivo PDK1 inhibition through a universally applicable RNAi approach for functional drug target validation in oncogenic pathway contexts. This approach, which relies on doxycycline-inducible shRNA expression from the Rosa26 locus, is ideal for functional studies of genes like PDK1 where constitutive mouse models lead to strong developmental phenotypes or embryonic lethality. We achieved more than 90% PDK1 knockdown in vivo, a level sufficient to impact physiological functions resulting in hyperinsulinemia and hyperglycemia. This phenotype was reversible on PDK1 reexpression. Unexpectedly, long-term PDK1 knockdown revealed a lack of potent antitumor efficacy in 3 different mouse models of PTEN-deficient cancer. Thus, despite efficient PDK1 knockdown, inhibition of the PI3K pathway was marginal suggesting that PDK1 was not a rate limiting factor. Ex vivo analysis of pharmacological inhibitors revealed that AKT and mTOR inhibitors undergoing clinical development are more effective than PDK1 inhibitors at blocking activated PI3K pathway signaling. Taken together our findings weaken the widely held expectation that PDK1 represents an appealing oncology target.
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7
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Margulies D, Opatowsky Y, Fletcher S, Saraogi I, Tsou LK, Saha S, Lax I, Schlessinger J, Hamilton AD. Surface binding inhibitors of the SCF-KIT protein-protein interaction. Chembiochem 2009; 10:1955-8. [PMID: 19637142 DOI: 10.1002/cbic.200900079] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- David Margulies
- Department of Chemistry, Yale University, New Haven, CT 06520-8107 (USA)
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8
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Nanochemie: Mirkin ausgezeichnet / Biochemie: Shokat geehrt / Theorie: Warshel gewählt. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Nanochemistry: Mirkin Awarded / Biochemistry: Shokat Honored / Theory: Warshel Elected. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/anie.200902658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Kumar N, Afeyan R, Kim HD, Lauffenburger DA. Multipathway model enables prediction of kinase inhibitor cross-talk effects on migration of Her2-overexpressing mammary epithelial cells. Mol Pharmacol 2008; 73:1668-78. [PMID: 18349105 DOI: 10.1124/mol.107.043794] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Small-molecule kinase inhibitors often modulate signaling pathways other than the one targeted, whether by direct "off-target" effects or by indirect "pathway cross-talk" effects. The presence of either or both of these classes of complicating factors impedes the predictive understanding of kinase inhibitor consequences for cell phenotypic behaviors involved in drug efficacy responses. To address this problem, we offer an avenue toward comprehending how kinase inhibitor modulations of cell signaling networks lead to altered cell phenotypic responses by applying a quantitative, multipathway computational modeling approach. We show that integrating measurements of signals across three key kinase pathways involved in regulating migration of human mammary epithelial cells, downstream of ErbB system receptor activation by epidermal growth factor (EGF) or heregulin (HRG), significantly improves prediction of cell migration changes resulting from treatment with the small-molecule inhibitors 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one (LY294002) and 2'-amino-3'-methoxyflavone (PD98059) for both normal and HER2-overexpressing cells. These inhibitors are primarily directed toward inhibition of phosphatidylinositol 3-kinase (PI3K) and mitogen-activated protein kinase kinase (MEK) but are known to exhibit off-target effects; moreover, complex cross-talk interactions between the PI3K/Akt and MEK/extracellular signal-regulated kinase (Erk) pathways are also appreciated. We observe here that treatment with LY294002 reduces migration of HRG-stimulated cells but not EGF-stimulated cells, despite comparable levels of reduction of Akt phosphorylation under both conditions, demonstrating that the target inhibition effect is not unilaterally predictive of efficacy against cell phenotypic response. Consequent measurement of levels of Erk and p38 phosphorylation, along with those for EGF receptor phosphorylation, after LY294002 treatment revealed unintended modulation of these nontargeted pathways. However, when these measurements were incorporated into a partial least-squares regression model, the cell migration responses to treatment were successfully predicted. Similar success was found for the same multipathway model in analogously predicting PD98059 treatment effects on cell migration. We conclude that a quantitative, multipathway modeling approach can provide a significant advance toward comprehending kinase inhibitor efficacy in the face of off-target and pathway cross-talk effects.
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Affiliation(s)
- Neil Kumar
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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11
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Perera BGK, Maly DJ. Design, synthesis and characterization of “clickable” 4-anilinoquinazoline kinase inhibitors. MOLECULAR BIOSYSTEMS 2008; 4:542-50. [DOI: 10.1039/b720014e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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12
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Page CS, Bates PA. Can MM-PBSA calculations predict the specificities of protein kinase inhibitors? J Comput Chem 2007; 27:1990-2007. [PMID: 17036304 DOI: 10.1002/jcc.20534] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
An application of the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) protocol to the prediction of protein kinase inhibitor selectivity is presented. Six different inhibitors are placed in equivalent orientations in each of six different receptors. Fully solvated molecular dynamics is then run for 1 ns on each of the 36 complexes, and the resulting trajectories scored, using the implicit solvent model. The results show some correlation with experimentally-determined specificities; anomalies may be attributed to a variety of causes, including difficulties in quantifying induced fit penalties and variabilities in normal modes calculations. Decomposing interaction energies on a per-residue basis yields more useful insights into the natures of the binding modes and suggests that the real value of such calculations lies in understanding interactions rather than outright prediction.
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Affiliation(s)
- Christopher S Page
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London, GB-WC2A 3PX, United Kingdom
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13
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Peifer C, Kinkel K, Abadleh M, Schollmeyer D, Laufer S. From five- to six-membered rings: 3,4-diarylquinolinone as lead for novel p38MAP kinase inhibitors. J Med Chem 2007; 50:1213-21. [PMID: 17323937 DOI: 10.1021/jm061097o] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this study we describe the design, synthesis, and biological evaluation of 3-(4-fluorophenyl)-4-pyridin-4-ylquinoline-2(1H)-one (5) as a new inhibitor of MAPK with a p38alphaMAPK IC50 of 1.8 muM. By keeping the common vicinal pyridine/4-F-phenyl pharmacophore, such as in prototypical imidazole 20 or isoxazole 13 but in 5 connected to the six-membered quinoline core, we were particularly interested in comparing biological activity, details of molecular geometry, and different binding modes of these compounds. Compounds 20 and 13 were active both in the p38alpha- and JNK3-assay, whereas 5 was selective for p38alpha, with no JNK3 inhibition. By comparing the X-ray structures of the compounds, we found a significantly larger distance between the pyridine and the 4-F-phenyl moiety in five-membered core structures relevant for ligand-protein interactions. Molecular modeling studies support the results based on differences in the ATP pockets of p38alpha and JNK3. Because most five-membered core based p38alpha inhibitors show also activity for JNK3, compound 5 is an interesting lead for selective p38alpha inhibitors.
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Affiliation(s)
- Christian Peifer
- Institute of Pharmacy, Department of Pharmaceutical and Medicinal Chemistry, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8/B, D-72076 Tübingen, Germany.
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14
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Verkhivker GM. In silico profiling of tyrosine kinases binding specificity and drug resistance using Monte Carlo simulations with the ensembles of protein kinase crystal structures. Biopolymers 2007; 85:333-48. [PMID: 17167796 DOI: 10.1002/bip.20656] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The molecular basis of the tyrosine kinases binding specificity and drug resistance against cancer drugs Imatinib and Dasatinib is elucidated using Monte Carlo simulations of the inhibitor-receptor binding with the ensembles of protein kinase crystal structures. In silico proteomics analysis unravels mechanisms by which structural plasticity of the tyrosine kinases is linked with the conformational preferences of Imatinib and Dasatinib in achieving effective drug binding with a distinct spectrum of the tyrosine kinome. The differences in the inhibitor sensitivities to the ABL kinase mutants are rationalized based on variations in the binding free energy profiles with the conformational states of the ABL kinase. While Imatinib binding is highly sensitive to the activation state of the enzyme, the computed binding profile of Dasatinib is remarkably tolerant to the conformational state of ABL. A comparative analysis of the inhibitor binding profiles with the clinically important ABL kinase mutants has revealed an excellent agreement with the biochemical and proteomics data. We have found that conformational adaptability of the kinase inhibitors to structurally different conformational states of the tyrosine kinases may have pharmacological relevance in acquiring a specific array of potent activities and regulating a scope of the inhibitor resistance mutations. This study outlines a useful approach for understanding and predicting the molecular basis of the inhibitor sensitivity against potential kinase targets and drug resistance.
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Affiliation(s)
- Gennady M Verkhivker
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, LA Jolla, CA 92093-0392, USA.
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15
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Boshoff HI, Dowd CS. Chemical genetics: an evolving toolbox for target identification and lead optimization. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2007; 64:49, 51-77. [PMID: 17195471 DOI: 10.1007/978-3-7643-7567-6_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemical genetics combines chemistry with biology as a means of exploring the function of unknown proteins or identifying the proteins responsible for a particular phenotype. Chemical genetics is thus a valuable tool in the identification of novel drug targets. This chapter describes the application of chemical genetics in traditional and systems-based approaches to drug target discovery and the tools/approaches that appear most promising for guiding future pharmaceutical development.
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16
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Peifer C, Krasowski A, Hämmerle N, Kohlbacher O, Dannhardt G, Totzke F, Schächtele C, Laufer S. Profile and Molecular Modeling of 3-(Indole-3-yl)-4-(3,4,5-trimethoxyphenyl)-1H-pyrrole-2,5dione (1) as a Highly Selective VEGF-R2/3 Inhibitor. J Med Chem 2006; 49:7549-53. [PMID: 17149885 DOI: 10.1021/jm0609871] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report on selectivity profiling of 1 in a panel of 20 protein kinases and molecular modeling indicating 1 to be highly active and selective for VEGF-R2/3. Sequence alignment analysis and detailed insights into the ATP binding pockets of targeted protein kinases from the panel result in a unique structural architecture of VEGF-R2 mainly caused by the hydrophobic pocket I, determining the molecular basis for activity and selectivity of 1.
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Affiliation(s)
- Christian Peifer
- Department of Pharmacy, Eberhard Karls University, Auf der Morgenstelle 8, D-72076 Tübingen, Germany.
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17
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Hooft van Huijsduijnen R, Rommel C. Decompartmentalizing target validation—thinking outside the pipeline boxes. J Mol Med (Berl) 2006; 84:802-13. [PMID: 16924470 DOI: 10.1007/s00109-006-0080-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 05/30/2006] [Indexed: 10/24/2022]
Affiliation(s)
- Rob Hooft van Huijsduijnen
- Serono Pharmaceutical Research Institute, Serono International S.A., 14, Chemin des Aulx, 1228, Plan-les-Ouates, Geneva, Switzerland
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18
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Abstract
Covalent modification of proteins by phosphorylation represents a major mechanism of signal transduction that contributes to many physiological and pathophysiological processes. The enzymes that regulate protein phosphorylation (e.g., protein kinases and phosphatases) are, therefore, potential targets for the rational design of small-molecule drugs for the treatment of many diseases. A critical aspect of drug design is the reliability of proof-of-principle studies that demonstrate the therapeutic potential of the drug target. Studies using genetically modified mouse models that lack expression of the drug target using gene ablation and RNAi-based technologies have been widely employed. Recently, an alternative strategy using a chemical genetic approach has been proposed. Here, the authors discuss the strengths and weaknesses of the chemical genetic approach for studies of target validation.
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Abstract
Chemical genomics is a powerful method to complement more traditional genetic techniques (i.e. knockout mice, siRNA) for the dissection of complex signaling networks. Wnt signaling in mammals is a complex and crucial regulator of diverse functions. The Wnt-beta-catenin pathway initiates a signaling cascade that is crucial in both normal development and the initiation and progression of cancer. A key step in Wnt activation of target genes is the nuclear translocation of beta-catenin and the formation of a complex between beta-catenin and members of the T-cell factor (TCF) family of transcription factors. Using a forward chemical genomics strategy, we identified ICG-001, a selective inhibitor of a subset of Wnt-beta-catenin-driven gene expression. This chemogenomic tool enables us to dissect this complex signaling network and to better understand the role of Wnt signaling in both normal and pathophysiological settings.
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20
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Fan QW, Weiss WA. Chemical genetic approaches to the development of cancer therapeutics. Curr Opin Genet Dev 2005; 16:85-91. [PMID: 16359858 DOI: 10.1016/j.gde.2005.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Accepted: 12/02/2005] [Indexed: 12/30/2022]
Abstract
Dysregulation of kinase-based signal transduction networks contributes to multiple aspects of malignancy. Chemical genetic approaches interrogate perturbed signaling in the immediate context of small molecule inhibitor treatment. In recent years, such approaches have identified new kinase targets, clarified the impact of poly-specific inhibition using agents for which at least one primary target is known, and have identified targets for which combinatorial inhibition leads to improved efficacy. Elucidation of the mechanisms through which specific small molecule drug-like agents impact crucial cancer pathways should yield important and clinically translatable insights into the use of similar agents in patients.
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MESH Headings
- Amino Acid Sequence
- Animals
- Genes, abl
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/etiology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Models, Biological
- Neoplasms/drug therapy
- Neoplasms/etiology
- Neoplasms/genetics
- Protein Kinases/genetics
- Sequence Homology, Amino Acid
- Signal Transduction/drug effects
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Affiliation(s)
- Qi-Wen Fan
- Department of Neurology, 533 Parnassus Avenue, San Francisco, CA 94143, USA
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21
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Berg T. Cellular Profiling of Small-Molecule Bioactivities: an Alternative Tool for Chemical Biology. Angew Chem Int Ed Engl 2005; 44:5008-11. [PMID: 15973752 DOI: 10.1002/anie.200500721] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Thorsten Berg
- Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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22
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Berg T. Zelluläre Profilierung der biologischen Aktivität niedermolekularer Substanzen - eine neue Methode für die chemische Biologie. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Lovrinovic M, Niemeyer CM. DNA-Mikroarrays als Decodierungswerkzeuge in der kombinatorischen Chemie und der chemischen Biologie. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500645] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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Lovrinovic M, Niemeyer CM. DNA Microarrays as Decoding Tools in Combinatorial Chemistry and Chemical Biology. Angew Chem Int Ed Engl 2005; 44:3179-83. [PMID: 15861437 DOI: 10.1002/anie.200500645] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marina Lovrinovic
- Universität Dortmund, Fachbereich Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Strasse 6, 44227 Dortmund, Germany
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