Genome-Wide Mapping of Cisplatin Damaged Gene Loci

2020 ◽  
Author(s):  
Luyu Qi ◽  
Qun Luo ◽  
Yan Xu ◽  
Wanchen Yu ◽  
Xingkai Liu ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Testicular Cancer ◽  
Protein Kinases ◽  
High Throughput Sequencing ◽  
Kinase Inhibitor ◽  
High Sensitivity ◽  
Affinity Isolation ◽  
Genome Wide ◽  
Transcription Regulators ◽  
Protein Kinase Signaling

AbstractCisplatin is a DNA targeting anticancer drug, yet its damaged gene loci have remained unclear. In the present work, combining affinity isolation and high throughput sequencing, we genome-widely mapped 17729 gene loci containing platination lesions, which mainly function as enzymes, transcription regulators, transporters and kinases, and of which 445 genes account for 71% of potential gene targets for cancer therapy reported in the literature. The most related core signaling pathway, disease and tissue toxicity of 7578 genes with an enrichment fold (EFG) of >12, where EFG refers to the ratio of total read counts of a gene detected in cells with and without cisplatin treatment, are sperm motility, cancer and hepatotoxicity with association P values of < 1×10−22. Among 616 kinase genes damaged by cisplatin, 427 are protein kinases which account for 82% of putative protein kinases, suggesting that cisplatin may act as broad-spectrum protein kinase inhibitor. Western Blot assays verified that expression of 8 important protein kinase genes was significantly reduced due to cisplatin damage. SPAG9 is closely related to 147 of 361 cancer diseases which the cisplatin damaged genes are associated with and was severely damaged by cisplatin. Given SPAG9 abundantly expresses JIP-4, a upstream mediator of protein kinase signaling, in testis, it may be responsible for the high sensitivity of testicular cancer to cisplatin, thus being a potential therapeutic target for precise treatment of testicular cancer. These findings provide novel insights into better understanding in molecular mechanism of anticancer activity and toxicity of cisplatin, more importantly inspire further studies in prioritizing gene targets for precise treatment of cancers.

scholarly journals Betulin, a Newly Characterized Compound in Acacia auriculiformis Bark, Is a Multi-Target Protein Kinase Inhibitor

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4599
Author(s):  
Augustine Ahmadu ◽  
Claire Delehouzé ◽  
Anas Haruna ◽  
Lukman Mustapha ◽  
Bilqis Lawal ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Kinase Inhibitor ◽  
Glycogen Synthase ◽  
Growth Factor Receptor ◽  
Binding Pocket ◽  
Stem Bark ◽  
Janus Kinase ◽  
Myelogenous Leukemia ◽  
Acacia Auriculiformis

The purpose of this work is to investigate the protein kinase inhibitory activity of constituents from Acacia auriculiformis stem bark. Column chromatography and NMR spectroscopy were used to purify and characterize betulin from an ethyl acetate soluble fraction of acacia bark. Betulin, a known inducer of apoptosis, was screened against a panel of 16 disease-related protein kinases. Betulin was shown to inhibit Abelson murine leukemia viral oncogene homolog 1 (ABL1) kinase, casein kinase 1ε (CK1ε), glycogen synthase kinase 3α/β (GSK-3 α/β), Janus kinase 3 (JAK3), NIMA Related Kinase 6 (NEK6), and vascular endothelial growth factor receptor 2 kinase (VEGFR2) with activities in the micromolar range for each. The effect of betulin on the cell viability of doxorubicin-resistant K562R chronic myelogenous leukemia cells was then verified to investigate its putative use as an anti-cancer compound. Betulin was shown to modulate the mitogen-activated protein (MAP) kinase pathway, with activity similar to that of imatinib mesylate, a known ABL1 kinase inhibitor. The interaction of betulin and ABL1 was studied by molecular docking, revealing an interaction of the inhibitor with the ABL1 ATP binding pocket. Together, these data demonstrate that betulin is a multi-target inhibitor of protein kinases, an activity that can contribute to the anticancer properties of the natural compound and to potential treatments for leukemia.

Imatinib quantification in human serum with LC-MS3 as an effective way of protein kinase inhibitor analysis in biological matrices

2017 ◽  
Vol 32 (3) ◽  
Author(s):  
Marek Dziadosz ◽  
Michael Klintschar ◽  
Jörg Teske
Keyword(s):  
Protein Kinase ◽  
Sample Preparation ◽  
Human Serum ◽  
Kinase Inhibitor ◽  
Limit Of Detection ◽  
High Sensitivity ◽  
Protein Kinase Inhibitor ◽  
Preparation Technique ◽  
Analytical Strategy ◽  
Inhibitor Analysis

AbstractBackground:As imatinib gained a lot of attention in the field of medicine, appropriate methods are needed for drug analysis. LC-MS/MS combined with complex sample preparation and column enrichment is usually the method of choice when high sensitivity is necessary. The application of LC-MSMethods:An LC-MSResults:The conditions applied resulted in a limit of detection/quantification value of 0.14/0.45 ng/mL reached without a sophisticated sample preparation technique or enrichment column application. It could be demonstrated that MSConclusions:The presented analytical strategy is an effective way of protein kinase inhibitor analysis in human serum.

scholarly journals Potential Role for Protein Kinases in Regulation of Bidirectional Endoplasmic Reticulum-to-Golgi Transport Revealed by Protein Kinase Inhibitor H89

2000 ◽  
Vol 11 (8) ◽  
pp. 2577-2590 ◽  
Author(s):  
Tina H. Lee ◽  
Adam D. Linstedt
Keyword(s):  
Endoplasmic Reticulum ◽  
Protein Kinase ◽  
Protein Kinase A ◽  
Protein Kinases ◽  
Potential Role ◽  
Kinase Inhibitor ◽  
Transport Processes ◽  
Protein Kinase Inhibitors ◽  
Er Export ◽  
Kinase A

Recent evidence suggests a regulatory connection between cell volume, endoplasmic reticulum (ER) export, and stimulated Golgi-to-ER transport. To investigate the potential role of protein kinases we tested a panel of protein kinase inhibitors for their effect on these steps. One inhibitor, H89, an isoquinolinesulfonamide that is commonly used as a selective protein kinase A inhibitor, blocked both ER export and hypo-osmotic-, brefeldin A-, or nocodazole-induced Golgi-to-ER transport. In contrast, H89 did not block the constitutive ER Golgi-intermediate compartment (ERGIC)-to-ER and Golgi-to-ER traffic that underlies redistribution of ERGIC and Golgi proteins into the ER after ER export arrest. Surprisingly, other protein kinase A inhibitors, KT5720 and H8, as well as a set of protein kinase C inhibitors, had no effect on these transport processes. To test whether H89 might act at the level of either the coatomer protein (COP)I or the COPII coat protein complex we examined the localization of βCOP and Sec13 in H89-treated cells. H89 treatment led to a rapid loss of Sec13-labeled ER export sites but βCOP localization to the Golgi was unaffected. To further investigate the effect of H89 on COPII we developed a COPII recruitment assay with permeabilized cells and found that H89 potently inhibited binding of exogenous Sec13 to ER export sites. This block occurred in the presence of guanosine-5′-O-(3-thio)triphosphate, suggesting that Sec13 recruitment is inhibited at a step independent of the activation of the GTPase Sar1. These results identify a requirement for an H89-sensitive factor(s), potentially a novel protein kinase, in recruitment of COPII to ER export sites, as well as in stimulated but not constitutive Golgi-to-ER transport.

scholarly journals Molecular Basis for Ser/Thr Specificity in PKA Signaling

Cells ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1548 ◽  
Author(s):  
Matthias J. Knape ◽  
Maximilian Wallbott ◽  
Nicole C. G. Burghardt ◽  
Daniela Bertinetti ◽  
Jan Hornung ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Substrate Specificity ◽  
Metal Ions ◽  
Protein Kinases ◽  
Molecular Basis ◽  
Kinase Inhibitor ◽  
Adenine Nucleotides ◽  
Catalytic Efficiency ◽  
Specific Protein ◽  
Divalent Metal Ions

cAMP-dependent protein kinase (PKA) is the major receptor of the second messenger cAMP and a prototype for Ser/Thr-specific protein kinases. Although PKA strongly prefers serine over threonine substrates, little is known about the molecular basis of this substrate specificity. We employ classical enzyme kinetics and a surface plasmon resonance (SPR)-based method to analyze each step of the kinase reaction. In the absence of divalent metal ions and nucleotides, PKA binds serine (PKS) and threonine (PKT) substrates, derived from the heat-stable protein kinase inhibitor (PKI), with similar affinities. However, in the presence of metal ions and adenine nucleotides, the Michaelis complex for PKT is unstable. PKA phosphorylates PKT with a higher turnover due to a faster dissociation of the product complex. Thus, threonine substrates are not necessarily poor substrates of PKA. Mutation of the DFG+1 phenylalanine to β-branched amino acids increases the catalytic efficiency of PKA for a threonine peptide substrate up to 200-fold. The PKA Cα mutant F187V forms a stable Michaelis complex with PKT and shows no preference for serine versus threonine substrates. Disease-associated mutations of the DFG+1 position in other protein kinases underline the importance of substrate specificity for keeping signaling pathways segregated and precisely regulated.

Ca(2+)-dependent protein kinases modulate proline transport across the renal brush-border membrane

1995 ◽  
Vol 268 (1) ◽  
pp. F155-F162 ◽  
Author(s):  
I. Zelikovic ◽  
J. Przekwas
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Brush Border ◽  
Brush Border Membrane ◽  
Kinase Inhibitor ◽  
Dependent Protein Kinase ◽  
Proline Transport ◽  
Renal Brush Border Membrane ◽  
Dependent Protein ◽  
Renal Brush Border

The cellular mechanisms controlling reabsorption of amino acids in the renal proximal tubule are unknown. Ca(2+)-dependent protein kinases modulate the activity of several ion channels and carriers in the kidney. The role of these enzymes in regulating tubular amino acid transport has not been established. We investigated the effect of Ca(2+)- and phospholipid-dependent protein kinase C (PKC) and Ca2+/calmodulin-dependent protein kinase II (CaMK II) on Na(+)- and Cl(-)-dependent proline transport across the rat renal brush-border membrane (BBM). Bioassays utilizing selective peptide substrates for Ca(2+)-dependent protein kinases demonstrated the presence of PKC and CaMK II in the BBM. Renal brush-border membrane vesicles (BBMV) were phosphorylated using the "hyposmotic shock" technique. Endogenous (membrane-bound) CaMK II and PKC, as well as exogenous, highly purified PKC inhibited NaCl-linked proline uptake by phosphorylated, lysed/resealed BBMV compared with control vesicles. The inhibitory effect of Ca2+ on proline transport, without the presence of other kinase activators, was mediated by activation of endogenous CaMK II. The CaMK II- and PKC-induced inhibition of proline uptake was reversed by the specific kinase inhibitor peptides CaMK II-(281-302) and PKC-(19-31), respectively. These data suggest that Ca(2+)-dependent protein kinase-mediated phosphorylation inhibits NaCl-dependent proline transport across the tubular luminal membrane.

scholarly journals Comparative Assessment of Protein Kinase Inhibitors in Public Databases and in PKIDB

Molecules ◽  
2020 ◽  
Vol 25 (14) ◽  
pp. 3226 ◽  
Author(s):  
Colin Bournez ◽  
Fabrice Carles ◽  
Gautier Peyrat ◽  
Samia Aci-Sèche ◽  
Stéphane Bourg ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Protein Kinase ◽  
Protein Kinases ◽  
Kinase Inhibitors ◽  
Kinase Inhibitor ◽  
Chemical Space ◽  
Principal Component ◽  
Great Majority ◽  
Protein Kinase Inhibitors ◽  
Principal Moments Of Inertia

Since the first approval of a protein kinase inhibitor (PKI) by the Food and Drug Administration (FDA) in 2001, 55 new PKIs have reached the market, and many inhibitors are currently being evaluated in clinical trials. This is a clear indication that protein kinases still represent major drug targets for the pharmaceutical industry. In a previous work, we have introduced PKIDB, a publicly available database, gathering PKIs that have already been approved (Phase 4), as well as those currently in clinical trials (Phases 0 to 3). This database is updated frequently, and an analysis of the new data is presented here. In addition, we compared the set of PKIs present in PKIDB with the PKIs in early preclinical studies found in ChEMBL, the largest publicly available chemical database. For each dataset, the distribution of physicochemical descriptors related to drug-likeness is presented. From these results, updated guidelines to prioritize compounds for targeting protein kinases are proposed. The results of a principal component analysis (PCA) show that the PKIDB dataset is fully encompassed within all PKIs found in the public database. This observation is reinforced by a principal moments of inertia (PMI) analysis of all molecules. Interestingly, we notice that PKIs in clinical trials tend to explore new 3D chemical space. While a great majority of PKIs is located on the area of “flatland”, we find few compounds exploring the 3D structural space. Finally, a scaffold diversity analysis of the two datasets, based on frequency counts was performed. The results give insight into the chemical space of PKIs, and can guide researchers to reach out new unexplored areas. PKIDB is freely accessible from the following website: http://www.icoa.fr/pkidb.

scholarly journals Major tegument protein VP8 of bovine herpesvirus 1 is phosphorylated by viral US3 and cellular CK2 protein kinases

2009 ◽  
Vol 90 (12) ◽  
pp. 2829-2839 ◽  
Author(s):  
Shaunivan L. Labiuk ◽  
Lorne A. Babiuk ◽  
Sylvia van Drunen Littel-van den Hurk
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Gene Product ◽  
Kinase Inhibitor ◽  
Bovine Herpesvirus ◽  
Kinase Assay ◽  
Bovine Herpesvirus 1 ◽  
Infected Cells ◽  
Herpesvirus 1

The UL47 gene product, VP8, is one of the major tegument proteins of bovine herpesvirus 1 (BoHV-1) and is subject to phosphorylation. Analysis of protein bands co-immunoprecipitated with VP8 from BoHV-1-infected cells by mass spectroscopy suggested that VP8 interacts with two protein kinases: cellular CK2 and viral US3. CK2 is a highly conserved cellular protein, expressed ubiquitously and known to phosphorylate numerous proteins. The US3 gene product is one of the viral kinases produced by BoHV-1 during infection. Interactions of CK2 and US3 with VP8 were confirmed outside the context of infection when FLAG–VP8 was expressed alone or co-expressed with US3–haemagglutinin tag in Cos-7 cells. Furthermore, VP8 and US3 were found to co-localize in the nucleus during viral infection. To explore the significance of these interactions, an in vitro kinase assay was performed, which demonstrated that VP8 is heavily phosphorylated by CK2. In the presence of the highly specific CK2 kinase inhibitor 2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole (DMAT), phosphorylation of VP8 was significantly reduced. Phosphorylation of VP8 was also inhibited by the presence of kenpaullone, a less specific CK2 inhibitor, but not by protein kinase CK1 or protein kinase C inhibitors. When VP8 and US3 were both included in the kinase assay in the presence of DMAT, phosphorylation of VP8 was again observed. Autophosphorylation of US3 was also detected and was not inhibited by DMAT. Based on these results, it is proposed that VP8 interacts with cellular CK2 and viral US3 in BoHV-1-infected cells, and is in turn subject to kinase activities associated with both of these proteins.

scholarly journals Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN

2021 ◽  
Author(s):  
Sheikh Nizamuddin ◽  
Stefanie Koidl ◽  
Tanja Bhuiyan ◽  
Tamara V Werner ◽  
Martin L Biniossek ◽  
...  
Keyword(s):  
Genome Mapping ◽  
Affinity Purification ◽  
High Sensitivity ◽  
Mapping Technique ◽  
Open Chromatin ◽  
Genome Wide ◽  
Genomic Scale ◽  
Transcription Regulators ◽  
Novel Method ◽  
Affinity Purification Mass Spectrometry

Abstract Genome-wide localization of chromatin and transcription regulators can be detected by a variety of techniques. Here, we describe a novel method ‘greenCUT&RUN’ for genome-wide profiling of transcription regulators, which has a very high sensitivity, resolution, accuracy and reproducibility, whilst assuring specificity. Our strategy begins with tagging of the protein of interest with GFP and utilizes a GFP-specific nanobody fused to MNase to profile genome-wide binding events. By using a GFP-nanobody the greenCUT&RUN approach eliminates antibody dependency and variability. Robust genomic profiles were obtained with greenCUT&RUN, which are accurate and unbiased towards open chromatin. By integrating greenCUT&RUN with nanobody-based affinity purification mass spectrometry, ‘piggy-back’ DNA binding events can be identified on a genomic scale. The unique design of greenCUT&RUN grants target protein flexibility and yields high resolution footprints. In addition, greenCUT&RUN allows rapid profiling of mutants of chromatin and transcription proteins. In conclusion, greenCUT&RUN is a widely applicable and versatile genome-mapping technique.

scholarly journals Sustained activation of p42/p44 mitogen-activated protein kinase during recovery from simulated ischaemia mediates adaptive cytoprotection in cardiomyocytes

2000 ◽  
Vol 350 (3) ◽  
pp. 891-899 ◽  
Author(s):  
Anu PUNN ◽  
James W. MOCKRIDGE ◽  
Saleha FAROOQUI ◽  
Michael S. MARBER ◽  
Richard J. HEADS
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
P38 Mapk ◽  
Cell Injury ◽  
Kinase Inhibitor ◽  
Mitogen Activated Protein Kinase ◽  
Neonatal Rat ◽  
Mitogen Activated Protein ◽  
Phosphoinositide 3 Kinase ◽  
Sustained Activation

Delayed cytoprotection (preconditioning) occurs 24h after sublethal simulated ischaemia and reperfusion (SI/R) in neonatal rat ventricular cardiomyocytes. SI/R was used to investigate the role of activation of mitogen-activated protein kinases (MAPKs), stress-activated protein kinases (SAPKs) and phosphoinositide 3-kinase-dependent protein kinase B (PKB)/Akt in cytoprotection. SI resulted in transient dual (Thr/Tyr) phosphorylation of p42/p44-MAPK and p38-MAPK, weak phosphorylation of p46/p54-SAPK, but no phosphorylation of PKB. ‘Reperfusion’ caused further transient phosphorylation of p38-MAPK, but sustained phosphorylation of p42/p44-MAPK (lasting 4h) and of Ser473 of PKB (lasting 2h). Furthermore, SI/R (24h) induced delayed protection against lethal SI, as determined by an increase in cell viability {bioreduction of MTT [3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide]} and a decrease in cell injury (release of creatine kinase). Both protection and phosphorylation of p42/p44-MAPK were blocked by the MEK-1/2 (MAPK/Erk kinase-1/2) inhibitor PD98059 (50µM) when given during SI/R, but not when given during SI alone. The p38-MAPK inhibitor SB203580 (10µM) blocked the p38-MAPK-dependent phosphorylation of activating transcription factor 2 in vitro, and the phosphoinositide 3-kinase inhibitor wortmannin (100nM) blocked PKB phosphorylation on Ser473. However, neither SB203580 nor wortmannin had any effect on delayed protection. Therefore sustained activation of p42/p44-MAPK during simulated ‘reperfusion’ following sublethal SI mediates preconditioning in cardiomyocytes independently of transient activation of p38-MAPK or sustained activation of PKB.

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