Current chemical genomics最新文献

{"title":"An agarose-gel based method for transporting cell lines.","authors":"Lingzhi Yang,&nbsp;Chufang Li,&nbsp;Ling Chen,&nbsp;Zhiyuan Li","doi":"10.2174/1875397300903010050","DOIUrl":"https://doi.org/10.2174/1875397300903010050","url":null,"abstract":"<p><p>Cryopreserved cells stored in dry ice or liquid nitrogen is the classical method for transporting cells between research laboratories in different cities around the world in order to maintain cell viability. An alternative method is to ship the live cells in flasks filled with cell culture medium. Both methods have limitations of either a requirement on special shipping container or short times for the cells to survive on the shipping process. We have recently developed an agarose gel based method for directly transporting the live adherent cells in cell culture plates or dishes in ambient temperature. This convenient method simplifies the transportation of live cells in long distance that can maintain cells in good viability for several days.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"3 ","pages":"50-3"},"PeriodicalIF":0.0,"publicationDate":"2009-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1c/32/TOCHGENJ-3-50.PMC2802760.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28718803","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":"A high throughput assay to identify small molecule modulators of prostatic acid phosphatase.","authors":"Rylan S Larsen,&nbsp;Mark J Zylka,&nbsp;John E Scott","doi":"10.2174/1875397300903010042","DOIUrl":"https://doi.org/10.2174/1875397300903010042","url":null,"abstract":"<p><p>Prostatic acid phosphatase (PAP) is expressed in nociceptive neurons and functions as an ectonucleotidase. Injection of the secretory isoform of PAP has potent antinociceptive effects in mouse models of chronic pain. These data suggested that a small molecule activator of PAP may have utility as a novel therapeutic for chronic pain, while inhibitors could be used to acutely inhibit PAP in vitro and in vivo. To identify small molecule modulators of PAP activity, we validated a high throughput, fluorescence-based biochemical assay and then used this assay to screen a compound library. We decreased the frequency of false positive activators by subtracting compound fluorescence from the final assay fluorescence. This approach significantly reduced the number of false positive activators found in the screen. While no activators were confirmed, seven novel inhibitors of PAP were identified. Our results suggest this high throughput assay could be used to identify small molecule modulators of PAP activity.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"3 ","pages":"42-9"},"PeriodicalIF":0.0,"publicationDate":"2009-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/3f/d9/TOCHGENJ-3-42.PMC2808025.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28718802","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":"In vitro viability and cytotoxicity testing and same-well multi-parametric combinations for high throughput screening.","authors":"Andrew L Niles,&nbsp;Richard A Moravec,&nbsp;Terry L Riss","doi":"10.2174/1875397300903010033","DOIUrl":"10.2174/1875397300903010033","url":null,"abstract":"<p><p>In vitro cytotoxicity testing has become an integral aspect of drug discovery because it is a convenient, costeffective, and predictive means of characterizing the toxic potential of new chemical entities. The early and routine implementation of this testing is testament to its prognostic importance for humans. Although a plethora of assay chemistries and methods exist for 96-well formats, few are practical and sufficiently sensitive enough for application in high throughput screening (HTS). Here we briefly describe a handful of the currently most robust and validated HTS assays for accurate and efficient assessment of cytotoxic risk. We also provide guidance for successful HTS implementation and discuss unique merits and detractions inherent in each method. Lastly, we discuss the advantages of combining specific HTS compatible assays into multi-parametric, same-well formats.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"3 ","pages":"33-41"},"PeriodicalIF":0.0,"publicationDate":"2009-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2174/1875397300903010033","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28717919","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":"HTRF: A technology tailored for drug discovery - a review of theoretical aspects and recent applications.","authors":"François Degorce,&nbsp;Amy Card,&nbsp;Sharon Soh,&nbsp;Eric Trinquet,&nbsp;Glenn P Knapik,&nbsp;Bing Xie","doi":"10.2174/1875397300903010022","DOIUrl":"https://doi.org/10.2174/1875397300903010022","url":null,"abstract":"<p><p>HTRF (Homogeneous Time Resolved Fluorescence) is the most frequently used generic assay technology to measure analytes in a homogenous format, which is the ideal platform used for drug target studies in high-throughput screening (HTS). This technology combines fluorescence resonance energy transfer technology (FRET) with time-resolved measurement (TR). In TR-FRET assays, a signal is generated through fluorescent resonance energy transfer between a donor and an acceptor molecule when in close proximity to each other. Buffer and media interference is dramatically reduced by dual-wavelength detection, and the final signal is proportional to the extent of product formation. The HTRF assay is usually sensitive and robust that can be miniaturized into the 384 and 1536-well plate formats. This assay technology has been applied to many antibody-based assays including GPCR signaling (cAMP and IP-One), kinases, cytokines and biomarkers, bioprocess (antibody and protein production), as well as the assays for protein-protein, proteinpeptide, and protein-DNA/RNA interactions.Since its introduction to the drug-screening world over ten years ago, researchers have used HTRF to expedite the study of GPCRs, kinases, new biomarkers, protein-protein interactions, and other targets of interest. HTRF has also been utilized as an alternative method for bioprocess monitoring. The first-generation HTRF technology, which uses Europium cryptate as a fluorescence donor to monitor reactions between biomolecules, was extended in 2008 through the introduction of a second-generation donor, Terbium cryptate (Tb), enhancing screening performance. Terbium cryptate possesses different photophysical properties compared to Europium, including increased quantum yield and a higher molar extinction coefficient. In addition to being compatible with the same acceptor fluorophors used with Europium, it can serve as a donor fluorophore to green-emitting fluors because it has multiple emission peaks including one at 490 nm. Moreover, all Terbium HTRF assays can be read on the same HTRF-compatible instruments as Europium HTRF assays.Overall, HTRF is a highly sensitive, robust technology for the detection of molecular interactions in vitro and is widely used for primary and secondary screening phases of drug development. This review addresses the general principles of HTRF and its current applications in drug discovery.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"3 ","pages":"22-32"},"PeriodicalIF":0.0,"publicationDate":"2009-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2174/1875397300903010022","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28717918","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":"Phenotypic fingerprinting of small molecule cell cycle kinase inhibitors for drug discovery.","authors":"Jonathan Low,&nbsp;Arunava Chakravartty,&nbsp;Wayne Blosser,&nbsp;Michele Dowless,&nbsp;Christopher Chalfant,&nbsp;Patty Bragger,&nbsp;Louis Stancato","doi":"10.2174/1875397300903010013","DOIUrl":"https://doi.org/10.2174/1875397300903010013","url":null,"abstract":"<p><p>Phenotypic drug discovery, primarily abandoned in the 1980's in favor of targeted approaches to drug development, is once again demonstrating its value when used in conjunction with new technologies. Phenotypic discovery has been brought back to the fore mainly due to recent advances in the field of high content imaging (HCI). HCI elucidates cellular responses using a combination of immunofluorescent assays and computer analysis which increase both the sensitivity and throughput of phenotypic assays. Although HCI data characterize cellular responses in individual cells, these data are usually analyzed as an aggregate of the treated population and are unable to discern differentially responsive subpopulations. A collection of 44 kinase inhibitors affecting cell cycle and apoptosis were characterized with a number of univariate, bivariate, and multivariate subpopulation analyses demonstrating that each level of complexity adds additional information about the treated populations and often distinguishes between compounds with seemingly similar mechanisms of action. Finally, these subpopulation data were used to characterize compounds as they relate in chemical space.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"3 ","pages":"13-21"},"PeriodicalIF":0.0,"publicationDate":"2009-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/63/e0/TOCHGENJ-3-13.PMC2793401.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28717917","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":"HTS-compatible beta-lactamase transcriptional reporter gene assay for interrogating the heat shock response pathway.","authors":"Michael K Hancock,&nbsp;Menghang Xia,&nbsp;Elizabeth S Frey,&nbsp;Srilatha Sakamuru,&nbsp;Kun Bi","doi":"10.2174/1875397300903010001","DOIUrl":"https://doi.org/10.2174/1875397300903010001","url":null,"abstract":"<p><p>Moderate environmental and physiological stressors are known to initiate protective heat shock response (HSR) leading to cell survival. HSR is largely mediated by the activation of heat shock factor (HSF), resulting in increased heat shock protein expression. Dysregulation of the HSR signaling has been associated with various diseases including cancer, inflammation and neurodegenerative disorders. Compounds that can modulate HSR have been pursued for the treatment of these diseases. To facilitate the discovery of HSR modulators, we developed a high-throughput amenable betalactamase transcriptional reporter gene assay for monitoring the function of HSF. HeLa cells were engineered to express the beta-lactamase reporter under the control of HSF response elements (HSE) present in the HSP70 gene promoter. The HSE-beta lactamase (HSE-bla) reporter gene assay was validated by using HSF-specific siRNAs and known small molecule modulators. Taking the advantage of fluorescence resonance energy transfer (FRET)-based cell permeable betalactamase substrate, this assay can be miniaturized into 1536-well format. Our results demonstrate that the assay is robust and can be applied to high-throughput screening (HTS) for modulators of HSR.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"3 ","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2009-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/40/f5/TOCHGENJ-3-1.PMC2793398.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28717916","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":"A Cell-based beta-Lactamase Reporter Gene Assay for the CREB Signaling Pathway.","authors":"Menghang Xia,&nbsp;Vicky Guo,&nbsp;Ruili Huang,&nbsp;James Inglese,&nbsp;Marshall Nirenberg,&nbsp;Christopher P Austin","doi":"10.2174/1875397300903010007","DOIUrl":"https://doi.org/10.2174/1875397300903010007","url":null,"abstract":"<p><p>The Cyclic-AMP Response Element Binding (CREB) proteins comprise a family of transcription factors that stimulate or repress the expression of a wide variety of genes by binding to nucleotide sequences known as cAMP Response Elements (CREs). CREB-mediated transcription has been implicated in a wide variety of important physiological processes, including long-term memory, and enhancement of CREB signaling has been suggested as an attractive therapeutic strategy for human memory disorders. To identify small molecule compounds that enhance CREB pathway signaling, we have optimized and validated a cell-based beta-lactamase reporter gene CREB pathway assay in 1536-well plate format. The LOPAC library of 1280 compounds was screened in triplicate in this assay on a quantitative high throughput screening (qHTS) platform. A variety of compounds which affect known members of the CREB pathway were identified as active, including twelve known phosphodiesterase (PDE) inhibitors, and forskolin, a known activator of adenylate cyclase, thus validating the assay's performance. This qHTS platform assay will facilitate identification of novel small molecule CREB signaling enhancers, which will be useful for chemical genetic dissection of the CREB pathway and as starting points for potentially memory-enhancing therapeutics.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"3 1","pages":"7-12"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c8/a0/TOCHGENJ-3-7.PMC2779037.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28527044","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":"Comparative docking assessment of glucokinase interactions with its allosteric activators.","authors":"Vandana Kumari,&nbsp;Chenglong Li","doi":"10.2174/1875397300802010076","DOIUrl":"https://doi.org/10.2174/1875397300802010076","url":null,"abstract":"<p><p>Glucokinase (GK) is expressed in multiple organs and plays a key role in hepatic glucose metabolism and pancreatic insulin secretion. GK could indeed serve as pacemaker of glycolysis and could be an attractive target for type 2 diabetes (T2D). The recent preclinical data of first GK activator RO-28-1675 has opened up a new field of GK activation as a powerful tool in T2D therapies. The GK allosteric site is located ~20A away from glucose binding site. Chemical structure of Glucokinase activators (GKA) includes three chemical arms; all consisting of cyclic moiety and joined in a shape resembling the letter Y. In this study, comparative docking assessment using Autodock4 revealed that the three arms bind to three aromatic/hydrophobic subpockets at the allosteric site. Our dockings have overall consistency with experimental data in both docking modes and simulated binding free energies, and offer insights on understanding GK/GKA interactions and further GKA design. Specifically, for the first pocket, involvement of Arg63 as key residue in two specific hydrogen-bond formations with all allosteric activators defines the binding feature; for the second pocket, it has the most diverse binding interactions, mostly aromatic, hydrophobic and multiple hydrogen bonds. The site has the best potential for further GKA optimization by utilizing aromatic heterocycles and hydrogen bond forming linkers to build the GKA 2(nd) arm.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"2 ","pages":"76-89"},"PeriodicalIF":0.0,"publicationDate":"2008-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2174/1875397300802010076","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28718756","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":"Development of fluorescence polarization assays for the molecular chaperone Hsp70 family members: Hsp72 and DnaK.","authors":"Laura Ricci,&nbsp;Kevin P Williams","doi":"10.2174/1875397300802010090","DOIUrl":"https://doi.org/10.2174/1875397300802010090","url":null,"abstract":"<p><p>The heat shock protein 70 (Hsp70) family of chaperones play crucial roles in protein folding and have been linked to numerous diseases. We were interested in developing a generally applicable assay format for the Hsp70 family and have developed fluorescence polarization based assays for both the mammalian Hsp72 and its bacterial counterpart, DnaK. These assays are comparable in assay set-up, incubation conditions and buffer components. Both unfolded polypeptides and synthetic peptides can be utilized as tracers to detect binding although peptides meeting the minimum seven residue length for Hsp70 binders have weaken binding when modified with fluorescein presumably due to steric effects. Although we did not identify a suitable general substrate for all Hsp70 proteins, fluorescein tagged peptide substrates that gave high affinity binding were identified for both DnaK and hsp72. We would predict that these assays will be suitable for identifying both selective chemical probes of Hsp70 family members and \"pan\" Hsp70 inhibitors.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"2 ","pages":"90-5"},"PeriodicalIF":0.0,"publicationDate":"2008-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0f/c8/TOCHGENJ-2-90.PMC2803438.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28718757","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":"A high throughput serum paraoxonase assay for discovery of small molecule modulators of PON1 activity.","authors":"Tiffany L Graves, John E Scott","doi":"10.2174/1875397300802010051","DOIUrl":"10.2174/1875397300802010051","url":null,"abstract":"<p><p>PON1 has been demonstrated to be the serum enzyme responsible for detoxifying organophosphate chemical weapons and plays a protective role against atherosclerosis. In order to identify small molecules that modulate PON1 activity in serum, we developed a high throughput kinetic absorbance assay using mouse serum and the organophosphate paraoxon. The IC(50) value obtained for the known PON1 inhibitor, 2-hydroxyquinoline, matched the value reported for purified PON1. A compound library was screened resulting in no confirmed activators, but 12 confirmed inhibitors. Seven of these hits also inhibited purified human PON1. One compound was only two-fold less potent than 2-hydroxyquinoline in the serum assay, but 10-fold more potent against purified PON1. This compound (IC(50) = 420 nM) may be useful towards a chemical probe for PON1. Therefore, this assay has utility as a high throughput assay for discovery of small molecule modulators of PON1 activity that maintain activity in serum.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"2 ","pages":"51-61"},"PeriodicalIF":0.0,"publicationDate":"2008-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2d/b8/TOCHGENJ-2-51.PMC2803440.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28718755","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}