BMC chemical biology最新文献

{"title":"Catalytic inhibition of topoisomerase II by a novel rationally designed ATP-competitive purine analogue","authors":"P. Chène, Joëlle Rudloff, J. Schoepfer, P. Furet, P. Meier, Zhiyan Qian, J. Schlaeppi, R. Schmitz, T. Radimerski","doi":"10.1186/1472-6769-9-1","DOIUrl":"https://doi.org/10.1186/1472-6769-9-1","url":null,"abstract":"","PeriodicalId":80682,"journal":{"name":"BMC chemical biology","volume":"9 1","pages":"1 - 1"},"PeriodicalIF":0.0,"publicationDate":"2009-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1472-6769-9-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65660568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chemogenetic fingerprinting by analysis of cellular growth dynamics.","authors":"Jonas Warringer,&nbsp;Dragi Anevski,&nbsp;Beidong Liu,&nbsp;Anders Blomberg","doi":"10.1186/1472-6769-8-3","DOIUrl":"https://doi.org/10.1186/1472-6769-8-3","url":null,"abstract":"<p><strong>Background: </strong>A fundamental goal in chemical biology is the elucidation of on- and off-target effects of drugs and biocides. To this aim chemogenetic screens that quantify drug induced changes in cellular fitness, typically taken as changes in composite growth, is commonly applied.</p><p><strong>Results: </strong>Using the model organism Saccharomyces cerevisiae we here report that resolving cellular growth dynamics into its individual components, growth lag, growth rate and growth efficiency, increases the predictive power of chemogenetic screens. Both in terms of drug-drug and gene-drug interactions did the individual growth variables capture distinct and only partially overlapping aspects of cell physiology. In fact, the impact on cellular growth dynamics represented functionally distinct chemical fingerprints.</p><p><strong>Discussion: </strong>Our findings suggest that the resolution and quantification of all facets of growth increases the informational and interpretational output of chemogenetic screening. Hence, by facilitating a physiologically more complete analysis of gene-drug and drug-drug interactions the here reported results may simplify the assignment of mode-of-action to orphan bioactive compounds.</p>","PeriodicalId":80682,"journal":{"name":"BMC chemical biology","volume":"8 ","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2008-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1472-6769-8-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27612278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Charting calcium-regulated apoptosis pathways using chemical biology: role of calmodulin kinase II.","authors":"Maria Hägg Olofsson,&nbsp;Aleksandra Mandic Havelka,&nbsp;Slavica Brnjic,&nbsp;Maria C Shoshan,&nbsp;Stig Linder","doi":"10.1186/1472-6769-8-2","DOIUrl":"https://doi.org/10.1186/1472-6769-8-2","url":null,"abstract":"<p><strong>Background: </strong>Intracellular free calcium ([Ca2+]i) is a key element in apoptotic signaling and a number of calcium-dependent apoptosis pathways have been described. We here used a chemical biology strategy to elucidate the relative importance of such different pathways.</p><p><strong>Results: </strong>A set of 40 agents (\"bioprobes\") that induce apoptosis was first identified by screening of a chemical library. Using p53, AP-1, NFAT and NF-kappaB reporter cell lines, these bioprobes were verified to induce different patterns of signaling. Experiments using the calcium chelator BAPTA-AM showed that Ca2+ was involved in induction of apoptosis by the majority of the bioprobes and that Ca2+ was in general required several hours into the apoptosis process. Further studies showed that the calmodulin pathway was an important mediator of the apoptotic response. Inhibition of calmodulin kinase II (CaMKII) resulted in more effective inhibition of apoptosis compared to inhibition of calpain, calcineurin/PP2B or DAP kinase. We used one of the bioprobes, the plant alkaloid helenalin, to study the role of CaMKII in apoptosis. Helenalin induced CaMKII, ASK1 and Jun-N-terminal kinase (JNK) activity, and inhibition of these kinases inhibited apoptosis.</p><p><strong>Conclusion: </strong>Our study shows that calcium signaling is generally not an early event during the apoptosis process and suggests that a CaMKII/ASK1 signaling mechanism is important for sustained JNK activation and apoptosis by some types of stimuli.</p>","PeriodicalId":80682,"journal":{"name":"BMC chemical biology","volume":"8 ","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2008-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1472-6769-8-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27573068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of cellular pathways affected by Sortin2, a synthetic compound that affects protein targeting to the vacuole in Saccharomyces cerevisiae.","authors":"Lorena Norambuena,&nbsp;Jan Zouhar,&nbsp;Glenn R Hicks,&nbsp;Natasha V Raikhel","doi":"10.1186/1472-6769-8-1","DOIUrl":"https://doi.org/10.1186/1472-6769-8-1","url":null,"abstract":"<p><strong>Background: </strong>Sortin2 is a low mass compound that interferes with vacuolar delivery of proteins in plants and yeast. The Sortin2 phenotype was tested in Arabidopsis thaliana and found to be reversible upon drug removal, demonstrating the ability of chemical genomics to induce reversible phenotypes that would be difficult to achieve using conventional genetics 1. However, standard genetic methods can be used to identify drug target pathways in a high-throughput manner.</p><p><strong>Results: </strong>In this study, we analyzed structure-function relationships of Sortin2 using structural analogues. The results show the key roles of sulphite substitution and a benzoic acid group. A Sortin 2 hypersensitivity screen for the induced secretion of a vacuolar cargo protein was done utilizing a yeast haploid deletion library. Using bioinformatics approaches, we highlighted functional information about the cellular pathways affected by drug treatment which included protein sorting and other endomembrane system-related processes.</p><p><strong>Conclusion: </strong>Chemical, genomic and genetics approaches were used to understand the mode of action of Sortin2, a bioactive chemical that affects the delivery of a vacuolar protein. Critical features of Sortin2 structure necessary for bioactivity suggest a binding pocket that may recognize two ends of Sortin2. The genome-wide screen shows that Sortin2 treatment in yeast affects primarily components within the endomembrane system. This approach allowed us to assign putative functions in protein sorting for fifteen genes of previously unknown function.</p>","PeriodicalId":80682,"journal":{"name":"BMC chemical biology","volume":"8 ","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2008-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1472-6769-8-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27210041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancement of intracellular gamma-tocopherol levels in cytokine-stimulated C3H 10T1/2 fibroblasts: relation to NO synthesis, isoprostane formation, and tocopherol oxidation.","authors":"Yuichiro Tanaka,&nbsp;Leslie A Lesoon Wood,&nbsp;Robert V Cooney","doi":"10.1186/1472-6769-7-2","DOIUrl":"https://doi.org/10.1186/1472-6769-7-2","url":null,"abstract":"<p><strong>Background: </strong>Stimulation of C3H 10T1/2 murine fibroblasts with interferon-gamma(IFN) and bacterial lipopolysaccharide (LPS) generates reactive oxygen and nitrogen species leading to DNA damage, lipid oxidation, and tocopherol oxidation. The tocopherols possess unique chemical and biological properties that suggest they have important roles related to intracellular defense against radical-mediated damage.</p><p><strong>Results: </strong>Despite increased levels of reactive oxidants and decreased media tocopherol, cellular levels of gamma-tocopherol, but not alpha-tocopherol, were observed to increase significantly when cells were treated with IFN/LPS. Inhibition of nitric oxide (NO) synthesis by a specific inhibitor of inducible NO synthase (iNOS) increased both intracellular alpha-tocopherol and gamma-tocopherol concentrations, but did not significantly alter the reduction in media tocopherol levels caused by IFN/LPS treatment. Both exposure to exogenous NO and cellular synthesis of NO in cell culture increased media levels of 8-epi-prostaglandin F2alpha, a marker of oxidative lipid damage, whereas inhibition of endogenous NO synthesis reduced media 8-epi-prostaglandin F2alpha formation to control levels.</p><p><strong>Conclusion: </strong>Elevated intracellular levels of gamma-tocopherol in response to the cellular inflammatory state may indicate that it serves a unique role in minimizing cellular damage resulting from endogenous NO synthesis. Results of the current study suggest that NO is an important mediator of damage within the cell, as well as in the oxidation of both alpha- and gamma-tocopherols. The paradoxical increase in cellular tocopherol associated with the induction of NO synthesis may indicate either enhanced cellular transport/decreased export for tocopherols or recruitment of free tocopherol from tocopherol storage molecules.</p>","PeriodicalId":80682,"journal":{"name":"BMC chemical biology","volume":"7 ","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2007-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1472-6769-7-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26812046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effect of amino acid deletions and substitutions in the longest loop of GFP.","authors":"Gabriela Flores-Ramírez,&nbsp;Manuel Rivera,&nbsp;Alfredo Morales-Pablos,&nbsp;Joel Osuna,&nbsp;Xavier Soberón,&nbsp;Paul Gaytán","doi":"10.1186/1472-6769-7-1","DOIUrl":"https://doi.org/10.1186/1472-6769-7-1","url":null,"abstract":"<p><strong>Background: </strong>The effect of single and multiple amino acid substitutions in the green fluorescent protein (GFP) from Aequorea victoria has been extensively explored, yielding several proteins of diverse spectral properties. However, the role of amino acid deletions in this protein -as with most proteins- is still unknown, due to the technical difficulties involved in generating combinatorial in-phase amino acid deletions on a target region.</p><p><strong>Results: </strong>In this study, the region I129-L142 of superglo GFP (sgGFP), corresponding to the longest loop of the protein and located far away from the central chromophore, was subjected to a random amino acid deletion approach, employing an in-house recently developed mutagenesis method termed Codon-Based Random Deletion (COBARDE). Only two mutants out of 16384 possible variant proteins retained fluorescence: sgGFP-Delta I129 and sgGFP-Delta D130. Interestingly, both mutants were thermosensitive and at 30 degrees C sgGFP-Delta D130 was more fluorescent than the parent protein. In contrast with deletions, substitutions of single amino acids from residues F131 to L142 were well tolerated. The substitution analysis revealed a particular importance of residues F131, G135, I137, L138, H140 and L142 for the stability of the protein.</p><p><strong>Conclusion: </strong>The behavior of GFP variants with both amino acid deletions and substitutions demonstrate that this loop is playing an important structural role in GFP folding. Some of the amino acids which tolerated any substitution but no deletion are simply acting as \"spacers\" to localize important residues in the protein structure.</p>","PeriodicalId":80682,"journal":{"name":"BMC chemical biology","volume":"7 ","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2007-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1472-6769-7-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26797409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Studies on the synthesis, characterization, binding with DNA and activities of two cis-planaramineplatinum(II) complexes of the form: cis-PtL(NH3)Cl2 where L = 3-hydroxypyridine and 2,3-diaminopyridine.","authors":"Ahmed Abdullah, Fazlul Huq, Ashraf Chowdhury, Hasan Tayyem, Philip Beale, Keith Fisher","doi":"10.1186/1472-6769-6-3","DOIUrl":"10.1186/1472-6769-6-3","url":null,"abstract":"<p><strong>Background: </strong>Cis-planaramineplatinum(II) complexes like their trans isomers are often found to be active against cancer cell lines. The present study deals with the synthesis, characterization and determination of activity of new cis-planaramineplatinum(II) complexes.</p><p><strong>Results: </strong>Two cis-planaramineplatinum(II) complexes: cis-(3-hydroxypyridine)(ammine)dichloroplatinum(II) (code named AH3) and cis-(2,3-diaminopyridine)(ammine)dichloroplatinum(II) (code named AH7) have been prepared and characterised based on elemental analyses, IR, Raman, mass and 1H NMR spectral measurements. The interactions of the compounds with pBR322 plasmid DNA have been investigated and their activity against ovarian cancer cell lines: A2780, A2780cisR and A2780ZD047Rhave been determined. Like cisplatin, AH3 and AH7 are believed to form mainly monofunctional N7(G) and bifunctional intrastrand N7(G)N7(G) adducts with DNA, causing a local distortion of a DNA strand. As a result, gel mobility of the DNA changes. Both AH3 and AH7 are found to be less active than cisplatin against the three cell lines with AH3 being the more active compound of the two. The higher activity of AH3 is in line with its lower molar conductivity value corresponding to a lower degree of dissociation.</p><p><strong>Conclusion: </strong>The differences in activity of AH3, AH7 and cisplatin against the cell lines illustrate structure-activity relationship.</p>","PeriodicalId":80682,"journal":{"name":"BMC chemical biology","volume":"6 ","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2006-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1431574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25902774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Small-molecule and mutational analysis of allosteric Eg5 inhibition by monastrol.","authors":"Zoltan Maliga,&nbsp;Timothy J Mitchison","doi":"10.1186/1472-6769-6-2","DOIUrl":"https://doi.org/10.1186/1472-6769-6-2","url":null,"abstract":"<p><strong>Background: </strong>A recent crystal structure of monastrol in a ternary complex with the kinesin Eg5 motor domain highlights a novel, induced-fit drug binding site at atomic resolution. Mutational obliteration of the monastrol binding site results in a monastrol-resistant, but otherwise catalytically active Eg5 motor domain. However, considering the conformational changes at this site, it is unclear what specific interactions stabilize the interaction between monastrol and the Eg5 motor domain.</p><p><strong>Results: </strong>To study the molecular complementarity of the monastrol-Eg5 interaction, we used a combination of synthetic chemistry and targeted mutations in Eg5 to measure the contribution of specific contacts to inhibition of Eg5 in vitro and in cultured cells. Structure-activity data on chemical derivatives, sequence analysis of Eg5 homologs from different species, and the effect of mutations near the drug binding site were consistent with the crystal structure.</p><p><strong>Conclusion: </strong>The mechanism of monastrol revealed by our data rationalizes its specificity for Eg5 over other kinesins and highlights a potential mechanism of drug resistance for anti-cancer therapy targeting this site in Eg5.</p>","PeriodicalId":80682,"journal":{"name":"BMC chemical biology","volume":"6 ","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2006-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1472-6769-6-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25878112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uncharged isocoumarin-based inhibitors of urokinase-type plasminogen activator.","authors":"Justin J Heynekamp,&nbsp;Lucy A Hunsaker,&nbsp;Thomas A Vander Jagt,&nbsp;Lorraine M Deck,&nbsp;David L Vander Jagt","doi":"10.1186/1472-6769-6-1","DOIUrl":"https://doi.org/10.1186/1472-6769-6-1","url":null,"abstract":"<p><strong>Background: </strong>Urokinase-type plasminogen activator (uPA) plays a major role in extracellular proteolytic events associated with tumor cell growth, migration and angiogenesis. Consequently, uPA is an attractive target for the development of small molecule active site inhibitors. Most of the recent drug development programs aimed at nonpeptidic inhibitors targeted at uPA have focused on arginino mimetics containing amidine or guanidine functional groups attached to aromatic or heterocyclic scaffolds. There is a general problem of limited bioavailability of these charged inhibitors. In the present study, uPA inhibitors were designed on an isocoumarin scaffold containing uncharged substituents.</p><p><strong>Results: </strong>4-Chloro-3-alkoxyisocoumarins were synthesized in which the 3-alkoxy group contained a terminal bromine; these were compared with similar inhibitors that contained a charged terminal functional group. Additional variations included functional groups attached to the seven position of the isocoumarin scaffold. N- [3-(3-Bromopropoxy)-4-chloro-1-oxo-1H-isochromen-7-yl]benzamide was identified as an uncharged lead inhibitor of uPA, Ki = 0.034 microM. Molecular modeling of human uPA with these uncharged inhibitors suggests that the bromine occupies the same position as positively charged arginino mimetic groups.</p><p><strong>Conclusion: </strong>This study demonstrates that potent uncharged inhibitors of uPA can be developed based upon the isocoumarin scaffold. A tethered bromine in the three position and an aromatic group in the seven position are important contributors to binding. Although the aim was to develop compounds that act as mechanism-based inactivators, these inhibitors are competitive reversible inhibitors.</p>","PeriodicalId":80682,"journal":{"name":"BMC chemical biology","volume":"6 ","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2006-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1472-6769-6-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25845474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Covalent attachment of the plant natural product naringenin to small glass and ceramic beads.","authors":"Yuhua Lu,&nbsp;Niloufer G Irani,&nbsp;Erich Grotewold","doi":"10.1186/1472-6769-5-3","DOIUrl":"https://doi.org/10.1186/1472-6769-5-3","url":null,"abstract":"<p><strong>Background: </strong>Natural products have numerous medicinal applications and play important roles in the biology of the organisms that accumulate them. Few methods are currently available for identifying proteins that bind to small molecules, therefore the discovery of cellular targets for natural products with pharmacological activity continues to pose a significant challenge in drug validation. Similarly, the identification of enzymes that participate in the biosynthesis or modification of natural products remains a formidable bottleneck for metabolic engineering. Flavonoids are one large group of natural products with a diverse number of functions in plants and in human health. The coupling of flavonoids to small ceramic and glass beads provides a first step in the development of high-throughput, solid-support base approaches to screen complex libraries to identify proteins that bind natural products.</p><p><strong>Results: </strong>The utilization of small glass and ceramic beads as solid supports for the coupling of small molecules was explored. Initial characterization of the beads indicated uniform and high capacity loading of amino groups. Once the beads were deemed adequate for the linking of small molecules by the coupling of NHS-fluorescein followed by microscopy, chemical hydrolysis and fluorometry, the flavonoid naringenin was modified with 1,4-dibromobutane, followed by the attachment of aminopropyltriethoxysilane. After NMR structural confirmation, the resulting 7-(4-(3-(triethoxysilyl)propylamino)butoxy) naringenin was attached to the ceramic beads.</p><p><strong>Conclusion: </strong>Our results demonstrate that ceramic and glass beads provide convenient solid supports for the efficient and facile coupling of small molecules. We succeeded in generating naringenin-coupled ceramic and glass beads. We also developed a convenient series of steps that can be applied for the solid-support coupling of other related flavonoids. The availability of solid-support coupled naringenin opens up new opportunities for the identification of flavonoid-binding proteins.</p>","PeriodicalId":80682,"journal":{"name":"BMC chemical biology","volume":"5 ","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2005-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1472-6769-5-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25628095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}