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Zhang H, He F, Gao G, Lu S, Wei Q, Hu H, Wu Z, Fang M, Wang X. Approved Small-Molecule ATP-Competitive Kinases Drugs Containing Indole/Azaindole/Oxindole Scaffolds: R&D and Binding Patterns Profiling. Molecules 2023; 28:molecules28030943. [PMID: 36770611 PMCID: PMC9920796 DOI: 10.3390/molecules28030943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
Kinases are among the most important families of biomolecules and play an essential role in the regulation of cell proliferation, apoptosis, metabolism, and other critical physiological processes. The dysregulation and gene mutation of kinases are linked to the occurrence and development of various human diseases, especially cancer. As a result, a growing number of small-molecule drugs based on kinase targets are being successfully developed and approved for the treatment of many diseases. The indole/azaindole/oxindole moieties are important key pharmacophores of many bioactive compounds and are generally used as excellent scaffolds for drug discovery in medicinal chemistry. To date, 30 ATP-competitive kinase inhibitors bearing the indole/azaindole/oxindole scaffold have been approved for the treatment of diseases. Herein, we summarize their research and development (R&D) process and describe their binding models to the ATP-binding sites of the target kinases. Moreover, we discuss the significant role of the indole/azaindole/oxindole skeletons in the interaction of their parent drug and target kinases, providing new medicinal chemistry inspiration and ideas for the subsequent development and optimization of kinase inhibitors.
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Affiliation(s)
- Haofan Zhang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Fengming He
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Guiping Gao
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
- School of Medicine, Huaqiao University, Quanzhou 362021, China
| | - Sheng Lu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Qiaochu Wei
- School of Public Health, Xiamen University, Xiamen 361102, China
| | - Hongyu Hu
- Xingzhi College, Zhejiang Normal University, Lanxi 321004, China
| | - Zhen Wu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Meijuan Fang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
- Correspondence: (M.F.); (X.W.)
| | - Xiumin Wang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
- Correspondence: (M.F.); (X.W.)
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2
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Breen ME, Soellner MB. Small molecule substrate phosphorylation site inhibitors of protein kinases: approaches and challenges. ACS Chem Biol 2015; 10:175-89. [PMID: 25494294 PMCID: PMC4301090 DOI: 10.1021/cb5008376] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Protein kinases are
important mediators of cellular communication
and attractive drug targets for many diseases. Although success has
been achieved with developing ATP-competitive kinase inhibitors, the
disadvantages of ATP-competitive inhibitors have led to increased
interest in targeting sites outside of the ATP binding pocket. Kinase
inhibitors with substrate-competitive, ATP-noncompetitive binding
modes are promising due to the possibility of increased selectivity
and better agreement between biochemical and in vitro potency. However, the difficulty of identifying these types of inhibitors
has resulted in significantly fewer small molecule substrate phosphorylation
site inhibitors being reported compared to ATP-competitive inhibitors.
This review surveys reported substrate phosphorylation site inhibitors
and methods that can be applied to the discovery of such inhibitors,
including a discussion of the challenges inherent to these screening
methods.
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Affiliation(s)
- Meghan E. Breen
- Department of Medicinal Chemistry and ‡Department of
Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Matthew B. Soellner
- Department of Medicinal Chemistry and ‡Department of
Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
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3
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English JG, Shellhammer JP, Malahe M, McCarter PC, Elston TC, Dohlman HG. MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast. Sci Signal 2015; 8:ra5. [PMID: 25587192 DOI: 10.1126/scisignal.2005774] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Signaling pathways can behave as switches or rheostats, generating binary or graded responses to a given cell stimulus. We evaluated whether a single signaling pathway can simultaneously encode a switch and a rheostat. We found that the kinase Hog1 mediated a bifurcated cellular response: Activation and commitment to adaptation to osmotic stress are switchlike, whereas protein induction and the resolution of this commitment are graded. Through experimentation, bioinformatics analysis, and computational modeling, we determined that graded recovery is encoded through feedback phosphorylation and a gene induction program that is both temporally staggered and variable across the population. This switch-to-rheostat signaling mechanism represents a versatile stress adaptation system, wherein a broad range of inputs generate an "all-in" response that is later tuned to allow graded recovery of individual cells over time.
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Affiliation(s)
- Justin G English
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - James P Shellhammer
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael Malahe
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Patrick C McCarter
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy C Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Henrik G Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Schwefel D, Daumke O. GTP-dependent scaffold formation in the GTPase of Immunity Associated Protein family. Small GTPases 2014; 2:27-30. [PMID: 21686278 DOI: 10.4161/sgtp.2.1.14938] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/19/2011] [Accepted: 01/20/2011] [Indexed: 11/19/2022] Open
Abstract
GTP ases of Immunity-Associated Proteins (GIMAPs) are a family of guanine nucleotide binding (G) proteins which are implicated in the regulation of apoptosis in lymphocytes. GIMAPs are composed of an amino-terminal G domain and carboxy-terminal extensions of varying size. Our recent biochemical and structural analysis of a representative GIMAP family member, GIMAP2, revealed the molecular basis of GTP-dependent oligomerization which involves two interfaces in the G domain. Whereas the amphipathic helix α7 in the C-terminal extension closely folds against the G domain in the GDP-bound state, it might be released in the GTP-bound state to assemble interaction partners. We also showed that the GIMAP2 oligomer functions at the surface of lipid droplets in a Jurkat T cell line. Here, we review our recent work and discuss the GIMAP2 oligomer as a GTP-dependent protein scaffold at the surface of lipid droplets controlling apoptosis.
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Affiliation(s)
- David Schwefel
- Max-Delbrück-Centrum für Molekulare Medizin; Freie Universität Berlin
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Galperin E, Abdelmoti L, Sorkin A. Shoc2 is targeted to late endosomes and required for Erk1/2 activation in EGF-stimulated cells. PLoS One 2012; 7:e36469. [PMID: 22606262 PMCID: PMC3351432 DOI: 10.1371/journal.pone.0036469] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 04/05/2012] [Indexed: 12/21/2022] Open
Abstract
Shoc2 is the putative scaffold protein that interacts with RAS and RAF, and positively regulates signaling to extracellular signal-regulated protein kinases 1 and 2 (ERK1/2). To elucidate the mechanism by which Shoc2 regulates ERK1/2 activation by the epidermal growth factor (EGF) receptor (EGFR), we studied subcellular localization of Shoc2. Upon EGFR activation, endogenous Shoc2 and red fluorescent protein tagged Shoc2 were translocated from the cytosol to a subset of late endosomes containing Rab7. The endosomal recruitment of Shoc2 was blocked by overexpression of a GDP-bound H-RAS (N17S) mutant and RNAi knockdown of clathrin, suggesting the requirement of RAS activity and clathrin-dependent endocytosis. RNAi depletion of Shoc2 strongly inhibited activation of ERK1/2 by low, physiological EGF concentrations, which was rescued by expression of wild-type recombinant Shoc2. In contrast, the Shoc2 (S2G) mutant, that is myristoylated and found in patients with the Noonan-like syndrome, did not rescue ERK1/2 activation in Shoc2-depleted cells. Shoc2 (S2G) was not located in late endosomes but was present on the plasma membrane and early endosomes. These data suggest that targeting of Shoc2 to late endosomes may facilitate EGFR-induced ERK activation under physiological conditions of cell stimulation by EGF, and therefore, may be involved in the spatiotemporal regulation of signaling through the RAS-RAF module.
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Affiliation(s)
- Emilia Galperin
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky, United States of America.
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Alexander RP, Lowenthal AC, Harshey RM, Ottemann KM. CheV: CheW-like coupling proteins at the core of the chemotaxis signaling network. Trends Microbiol 2010; 18:494-503. [PMID: 20832320 DOI: 10.1016/j.tim.2010.07.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 07/13/2010] [Accepted: 07/26/2010] [Indexed: 11/26/2022]
Abstract
Microbes have chemotactic signaling systems that enable them to detect and follow chemical gradients in their environments. The core of these sensory systems consists of chemoreceptor proteins coupled to the CheA kinase via the scaffold or coupler protein CheW. Some bacterial chemotaxis systems replace or augment CheW with a related protein, CheV, which is less well understood. CheV consists of a CheW domain fused to a receiver domain that is capable of being phosphorylated. Our review of the literature, as well as comparisons of the CheV and CheW sequence and structure, suggest that CheV proteins conserve CheW residues that are crucial for coupling. Phosphorylation of the CheV receiver domain might adjust the efficiency of its coupling and thus allow the system to modulate the response to chemical stimuli in an adaptation process.
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Affiliation(s)
- Roger P Alexander
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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Thalhauser CJ, Komarova NL. Signal response sensitivity in the yeast mitogen-activated protein kinase cascade. PLoS One 2010; 5:e11568. [PMID: 20668519 PMCID: PMC2909145 DOI: 10.1371/journal.pone.0011568] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 06/01/2010] [Indexed: 11/29/2022] Open
Abstract
The yeast pheromone response pathway is a canonical three-step mitogen activated protein kinase (MAPK) cascade which requires a scaffold protein for proper signal transduction. Recent experimental studies into the role the scaffold plays in modulating the character of the transduced signal, show that the presence of the scaffold increases the biphasic nature of the signal response. This runs contrary to prior theoretical investigations into how scaffolds function. We describe a mathematical model of the yeast MAPK cascade specifically designed to capture the experimental conditions and results of these empirical studies. We demonstrate how the system can exhibit either graded or ultrasensitive (biphasic) response dynamics based on the binding kinetics of enzymes to the scaffold. At the basis of our theory is an analytical result that weak interactions make the response biphasic while tight interactions lead to a graded response. We then show via an analysis of the kinetic binding rate constants how the results of experimental manipulations, modeled as changes to certain of these binding constants, lead to predictions of pathway output consistent with experimental observations. We demonstrate how the results of these experimental manipulations are consistent within the framework of our theoretical treatment of this scaffold-dependent MAPK cascades, and how future efforts in this style of systems biology can be used to interpret the results of other signal transduction observations.
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Affiliation(s)
- Craig J. Thalhauser
- Department of Mathematics, University of California Irvine, Irvine, California, United States of America
| | - Natalia L. Komarova
- Department of Mathematics, University of California Irvine, Irvine, California, United States of America
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Beta-Adrenergic Agonists. Pharmaceuticals (Basel) 2010; 3:1016-1044. [PMID: 27713285 PMCID: PMC4034018 DOI: 10.3390/ph3041016] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 03/15/2010] [Accepted: 03/26/2010] [Indexed: 12/31/2022] Open
Abstract
Inhaled β2-adrenoceptor (β2-AR) agonists are considered essential bronchodilator drugs in the treatment of bronchial asthma, both as symptoms-relievers and, in combination with inhaled corticosteroids, as disease-controllers. In this article, we first review the basic mechanisms by which the β2-adrenergic system contributes to the control of airway smooth muscle tone. Then, we go on describing the structural characteristics of β2-AR and the molecular basis of G-protein-coupled receptor signaling and mechanisms of its desensitization/ dysfunction. In particular, phosphorylation mediated by protein kinase A and β-adrenergic receptor kinase are examined in detail. Finally, we discuss the pivotal role of inhaled β2-AR agonists in the treatment of asthma and the concerns about their safety that have been recently raised.
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Corcelle EA, Puustinen P, Jäättelä M. Apoptosis and autophagy: Targeting autophagy signalling in cancer cells -'trick or treats'? FEBS J 2009; 276:6084-96. [PMID: 19788415 DOI: 10.1111/j.1742-4658.2009.07332.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Macroautophagy (hereafter referred to as autophagy) is a tightly regulated lysosome-dependent catabolic pathway. During this process, cytosolic constituents are sequestered into autophagosomes, which subsequently fuse with lysosomes to become autolysosomes, where their contents are degraded. Autophagy contributes to the maintenance of the cellular energy homeostasis, to the clearance of damaged organelles and to adaptation to environmental stresses. Accordingly, autophagy defects have been linked to a wide range of human pathologies, including cancer. The recent discovery of several evolutionarily conserved genes involved in autophagosome formation has greatly stimulated the autophagy research, and the complex signalling networks regulating mammalian autophagy have begun to emerge. Here, we draw the current picture of signalling pathways connecting mitogenic and stress-induced signals to the initiation and maturation of autophagosomes and discuss the possibilities of their targeting as therapeutic adjuvants in anticancer therapy.
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Affiliation(s)
- Elisabeth A Corcelle
- Apoptosis Department and Centre for Genotoxic Stress Research, Institute of Cancer Biology, Danish Cancer Society, Copenhagen, Denmark
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10
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Miyatake M, Rubinstein TJ, McLennan GP, Belcheva MM, Coscia CJ. Inhibition of EGF-induced ERK/MAP kinase-mediated astrocyte proliferation by mu opioids: integration of G protein and beta-arrestin 2-dependent pathways. J Neurochem 2009; 110:662-74. [PMID: 19457093 DOI: 10.1111/j.1471-4159.2009.06156.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although micro, kappa, and delta opioids activate extracellular signal-regulated kinase (ERK)/mitogen-activated protein (MAP) kinase, the mechanisms involved in their signaling pathways and the cellular responses that ensue differ. Here we focused on the mechanisms by which micro opioids rapidly (min) activate ERK and their slower (h) actions to inhibit epidermal growth factor (EGF)-induced ERK-mediated astrocyte proliferation. The micro-opioid agonists ([d-ala(2), mephe(4), gly-ol(5)] enkephalin and morphine) promoted the phosphorylation of ERK/MAP kinase within 5 min via G(i/o) protein, calmodulin (CaM), and beta-arrestin2-dependent signaling pathways in immortalized and primary astrocytes. This was based on the attenuation of the micro-opioid activation of ERK by pertussis toxin (PTX), the CaM antagonist, W-7, and siRNA silencing of beta-arrestin2. All three pathways were shown to activate ERK via an EGF receptor transactivation-mediated mechanism. This was disclosed by abolishment of micro-opioid-induced ERK phosphorylation with the EGF receptor-specific tyrosine phosphorylation inhibitor, AG1478, and micro-opioid-induced reduction of EGF receptor tyrosine phosphorylation by PTX, and beta-arrestin2 targeting siRNA in the present studies and formerly by CaM antisense. Long-term (h) treatment of primary astrocytes with [d-ala(2),mephe(4),gly-ol(5)] enkephalin or morphine, attenuated EGF-induced ERK phosphorylation and proliferation (as measured by 5'-bromo-2'-deoxy-uridine labeling). PTX and beta-arrestin2 siRNA but not W-7 reversed the micro-opioid inhibition. Unexpectedly, beta-arrestin-2 siRNA diminished both EGF-induced ERK activation and primary astrocyte proliferation suggesting that this adaptor protein plays a novel role in EGF signaling as well as in the opioid receptor phase of this pathway. The results lend insight into the integration of the different micro-opioid signaling pathways to ERK and their cellular responses.
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Affiliation(s)
- Mayumi Miyatake
- E. A. Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, Missouri 63104, USA
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Ma B, Nussinov R. Amplification of signaling via cellular allosteric relay and protein disorder. Proc Natl Acad Sci U S A 2009; 106:6887-8. [PMID: 19416924 PMCID: PMC2678435 DOI: 10.1073/pnas.0903024106] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Buyong Ma
- Basic Research Program, Center for Cancer Research Nanobiology Program, SAIC-Frederick, National Cancer Institute, Frederick, MD 21702; and
| | - Ruth Nussinov
- Basic Research Program, Center for Cancer Research Nanobiology Program, SAIC-Frederick, National Cancer Institute, Frederick, MD 21702; and
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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