Current chemical genomics最新文献

{"title":"A novel fluorogenic coumarin substrate for monitoring acid phosphatase activity at low pH environment.","authors":"Desuo Yang,&nbsp;Zongxiao Li,&nbsp;Yubo Allan Diwu,&nbsp;Hanzhuo Fu,&nbsp;Jinfang Liao,&nbsp;Chunmei Wei,&nbsp;Zhenjun Diwu","doi":"10.2174/1875397300802010048","DOIUrl":"https://doi.org/10.2174/1875397300802010048","url":null,"abstract":"<p><p>This article described the synthesis and application of 6-chloro-8-fluoro-4-methylumbelliferone phosphate (CF-MUP) in analyzing acid phosphatase activity. Compared to the existing MUP, the new coumarin phosphate, CF-MUP, demonstrateed much higher sensitivity and was more robust for detecting the activity of acid phosphatase than the classic substrate 4-methylumbelliferone phosphate (MUP). The product of enzyme reaction, 6-chloro-8-fluoro-4-methylumbelliferone (CF-MU) possesses strong fluorescence at approximately 450 nm with low pKa (4.7), high fluorescence quantum yield and pH independence in the physiological pH range. This new fluorescence dye, CF-MU, is a convenient tool for assays with buffer pH between 4.5 and 8.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"2 ","pages":"48-50"},"PeriodicalIF":0.0,"publicationDate":"2008-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/8e/90/TOCHGENJ-2-48.PMC2803437.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28718754","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 homogenous luminescent proximity assay for 14-3-3 interactions with both phosphorylated and nonphosphorylated client peptides.","authors":"Yuhong Du,&nbsp;Fadlo R Khuri,&nbsp;Haian Fu","doi":"10.2174/1875397300802010040","DOIUrl":"https://doi.org/10.2174/1875397300802010040","url":null,"abstract":"<p><p>The 14-3-3 proteins are a family of dimeric eukaryotic proteins that mediate both phosphorylation-dependent and -independent protein-protein interactions. Through these interactions, 14-3-3 proteins participate in the regulation of a wide range of cellular processes, including cell proliferation, cell cycle progression, and apoptosis. Because of their fundamental importance, 14-3-3 proteins have also been implicated in a variety of diseases, including cancer and neurodegenerative disorders. In order to monitor 14-3-3/client protein interactions for the discovery of small molecule 14-3-3 modulators, we have designed and optimized 14-3-3 protein binding assays based on the amplified luminescent proximity homogeneous assay (AlphaScreen) technology. Using the interaction of 14-3-3 with a phosphorylated Raf-1 peptide and a nonphosphorylated R18 peptide as model systems, we have established homogenous \"add-and-measure\" high-throughput screening assays. Both assays achieved robust performance with S/B ratios above 7 and Z' factors above 0.7. Application of the known antagonistic peptides in our studies further validated the assay for screening of chemical compound libraries to identify small molecules that can modulate 14-3-3 protein-protein interactions.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"2 ","pages":"40-7"},"PeriodicalIF":0.0,"publicationDate":"2008-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e5/e9/TOCHGENJ-2-40.PMC2803432.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28718809","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 new structure-based QSAR method affords both descriptive and predictive models for phosphodiesterase-4 inhibitors.","authors":"Xialan Dong,&nbsp;Weifan Zheng","doi":"10.2174/1875397300802010029","DOIUrl":"https://doi.org/10.2174/1875397300802010029","url":null,"abstract":"<p><p>We describe the application of a new QSAR (quantitative structure-activity relationship) formalism to the analysis and modeling of PDE-4 inhibitors. This new method takes advantage of the X-ray structural information of the PDE-4 enzyme to characterize the small molecule inhibitors. It calculates molecular descriptors based on the matching of their pharmacophore feature pairs with those (the reference) of the target binding pocket. Since the reference is derived from the X-ray crystal structures of the target under study, these descriptors are target-specific and easy to interpret. We have analyzed 35 indole derivative-based PDE-4 inhibitors where Partial Least Square (PLS) analysis has been employed to obtain the predictive models. Compared to traditional QSAR methods such as CoMFA and CoMSIA, our models are more robust and predictive measured by statistics for both the training and test sets of molecules. Our method can also identify critical pharmacophore features that are responsible for the inhibitory potency of the small molecules. Thus, this structure-based QSAR method affords both descriptive and predictive models for phosphodiesterase-4 inhibitors. The success of this study has also laid a solid foundation for systematic QSAR modeling of the PDE family of enzymes, which will ultimately contribute to chemical genomics research and drug discovery targeting the PDE enzymes.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"2 ","pages":"29-39"},"PeriodicalIF":0.0,"publicationDate":"2008-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b3/b1/TOCHGENJ-2-29.PMC2803435.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28718808","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 novel bioluminescent protease assay using engineered firefly luciferase.","authors":"Susan S Wigdal,&nbsp;Jessica L Anderson,&nbsp;Gediminas J Vidugiris,&nbsp;John Shultz,&nbsp;Keith V Wood,&nbsp;Frank Fan","doi":"10.2174/1875397300802010016","DOIUrl":"https://doi.org/10.2174/1875397300802010016","url":null,"abstract":"<p><p>Proteases play important roles in a variety of disease processes. Understanding their biological functions underpins the efforts of drug discovery. We have developed a bioluminescent protease assay using a circularly permuted form of firefly luciferase, wherein the native enzyme termini were joined by a peptide containing a protease site of interest. Protease cleavage of these mutant luciferases greatly activates the enzyme, typically over 100 fold. The mutant luciferase substrates are easily generated by molecular cloning and cell-free translation reactions and thus the protease substrates do not need to be chemically synthesized or purchased. The assay has broad applicability using a variety of proteases and their cognate sites and can sensitively detect protease activity. In this report we further demonstrate its utility for the evaluation of protease recognition sequence specificity and subsequent establishment of an optimized assay for the identification and characterization of protease inhibitors using high throughput screening.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"2 ","pages":"16-28"},"PeriodicalIF":0.0,"publicationDate":"2008-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0c/71/TOCHGENJ-2-16.PMC2803436.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28718807","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":"Improvements in live cell analysis of G protein coupled receptors using second generation BD calcium assay kits.","authors":"Xiao Li,&nbsp;Isabel Llorente,&nbsp;Mike Brasch","doi":"10.2174/1875397300802010010","DOIUrl":"https://doi.org/10.2174/1875397300802010010","url":null,"abstract":"<p><p>BD Calcium Assay Kits are designed for cell-based calcium mobilization high-throughput screening assays. The kits use a proprietary formulation including a non-fluorescent calcium indicator that becomes activated inside the cell and shows increased fluorescence upon calcium binding. The formulation includes a signal-enhancing reagent to maximize the signal over background in a homogeneous, no-wash assay format, based on a technology developed at BD. We have compared the next generation BD calcium assay kit product family to previous versions of the formulation, and to other commercially available homogeneous calcium assay kits. The improvements have enabled better performance on the cell lines and receptors that we have tested in all plate formats including 1536.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"2 ","pages":"10-5"},"PeriodicalIF":0.0,"publicationDate":"2008-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a2/30/TOCHGENJ-2-10.PMC2803433.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28718806","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":"Inhibition of inducible nitric oxide synthase expression by a novel small molecule activator of the unfolded protein response.","authors":"Kent T Symons,&nbsp;Mark E Massari,&nbsp;Sara J Dozier,&nbsp;Phan M Nguyen,&nbsp;David Jenkins,&nbsp;Mark Herbert,&nbsp;Timothy C Gahman,&nbsp;Stewart A Noble,&nbsp;Natasha Rozenkrants,&nbsp;Yan Zhang,&nbsp;Tadimeti S Rao,&nbsp;Andrew K Shiau,&nbsp;Christian A Hassig","doi":"10.2174/1875397300802010001","DOIUrl":"https://doi.org/10.2174/1875397300802010001","url":null,"abstract":"<p><p>The transcription of inducible nitric oxide synthase (iNOS) is activated by a network of proinflammatory signaling pathways. Here we describe the identification of a small molecule that downregulates the expression of iNOS mRNA and protein in cytokine-activated cells and suppresses nitric oxide production in vivo. Mechanistic analysis suggests that this small molecule, erstressin, also activates the unfolded protein response (UPR), a signaling pathway triggered by endoplasmic reticulum stress. Erstressin induces rapid phosphorylation of eIF2alpha and the alternative splicing of XBP-1, hallmark initiating events of the UPR. Further, erstressin activates the transcription of multiple genes involved in the UPR. These data suggest an inverse relationship between UPR activation and iNOS mRNA and protein expression under proinflammatory conditions.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"2 ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2008-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f6/b1/TOCHGENJ-2-1.PMC2803434.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28718805","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":"Comparison on functional assays for Gq-coupled GPCRs by measuring inositol monophospate-1 and intracellular calcium in 1536-well plate format.","authors":"Ke Liu,&nbsp;Steve Titus,&nbsp;Noel Southall,&nbsp;Pingjun Zhu,&nbsp;James Inglese,&nbsp;Christopher P Austin,&nbsp;Wei Zheng","doi":"10.2174/1875397300801010070","DOIUrl":"https://doi.org/10.2174/1875397300801010070","url":null,"abstract":"<p><p>Cell-based functional assays used for compound screening and lead optimization play an important role in drug discovery for G-protein coupled receptors (GPCRs). Cell-based assays can define the role of a compound as an agonist, antagonist or inverse agonist and can provide detailed information about the potency and efficacy of a compound. In addition, cell-based screens can be used to identify allosteric modulators that interact with sites other than the binding site of the endogenous ligand. Intracellular calcium assays which use a fluorescent calcium binding dye (such as Fluo-3, Fluo-4 or Fura-2) have been used in compound screening campaigns to measure the activity of Gq-coupled GPCRs. However, such screening methodologies require a special instrumentation to record the rapid change in intracellular free calcium concentration over time. The radioactive inositol 1,4,5- triphosphate (IP(3)) assay measures (3)H-inositol incorporation and is another traditional assay for the assessment of Gq-coupled GPCR activity, but it is not suitable for screening of large size compound collections because it requires a cell wash step and generates radioactive waste. To avoid these limitations, we have optimized and miniaturized a TR-FRET based IP-One assay that measures inositol monophosphate in a 1536-well plate format. This assay is homogenous, non-radioactive and does not require a kinetic readout. It has been tested with the cell lines expressing M(1) acetylcholine, FFAR1, vasopressin V1b, or Neuropeptide S receptors. The activities of antagonists determined in the IP-One assay correlated well with these measured in the intracellular calcium assay while the correlation of agonist activities might vary from cell line to cell line. This IP-One assay offers an alternative method for high throughput screening of Gq-coupled GPCRs without using costly kinetic plate readers.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"1 ","pages":"70-8"},"PeriodicalIF":0.0,"publicationDate":"2008-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28717915","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 imaging probe development center and the production of molecular imaging probes.","authors":"Gary L Griffiths","doi":"10.2174/1875397300801010065","DOIUrl":"https://doi.org/10.2174/1875397300801010065","url":null,"abstract":"<p><p>The Imaging Probe Development Center (IPDC), part of the NIH Roadmap for Medical Research Initiative (http://nihroadmap.nih.gov/) recently became fully operational at its newly refurbished laboratories in Rockville, MD. The IPDC (http://nihroadmap.nih.gov/molecularlibraries/ipdc/) is dedicated to the production of known and novel molecular imaging probes, with its services currently being used by the NIH intramural community, although in the future it is intended that the extramural community will also benefit from the IPDC's resources. The Center has been set up with the belief that molecular imaging, and the probe chemistry that underpins it, will constitute key technologies going forward. As part of the larger molecular libraries and imaging initiative, it is planned that the IPDC will work closely with scientists from the molecular libraries effort. Probes produced at the IPDC include optical, radionuclide and magnetic resonance agents and may encompass any type of contrast agent. As IPDC is a trans-NIH resource it can serve each of the 27 Institutes and Centers that comprise NIH so its influence can be expected to impact widely different subjects and disease conditions spanning biological research. IPDC is expected to play a key part in interdisciplinary collaborative imaging projects and to support translational R&D from basic research through clinical development, for all of the imaging modalities. Examples of probes already prepared or under preparation are outlined to illustrate the breadth of the chemistries undertaken together with a reference outline of the diverse biological applications for which the various probes are intended.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"1 ","pages":"65-9"},"PeriodicalIF":0.0,"publicationDate":"2008-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28717914","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":"Cellular Ser/Thr-kinase assays using generic peptide substrates.","authors":"Deanna G Adams,&nbsp;Yu Wang,&nbsp;Puiying A Mak,&nbsp;Jason Chyba,&nbsp;Orzala Shalizi,&nbsp;Jason Matzen,&nbsp;Paul Anderson,&nbsp;Tim R Smith,&nbsp;Michael Garcia,&nbsp;Genevieve L Welch,&nbsp;Emmanuel J Claret,&nbsp;Michel Fink,&nbsp;Anthony P Orth,&nbsp;Jeremy S Caldwell,&nbsp;Achim Brinker","doi":"10.2174/1875397300801010054","DOIUrl":"https://doi.org/10.2174/1875397300801010054","url":null,"abstract":"<p><p>High-throughput cellular profiling has successfully stimulated early drug discovery pipelines by facilitating targeted as well as opportunistic lead finding, hit annotation and SAR analysis. While automation-friendly universal assay formats exist to address most established drug target classes like GPCRs, NHRs, ion channels or Tyr-kinases, no such cellular assay technology is currently enabling an equally broad and rapid interrogation of the Ser/Thr-kinase space. Here we present the foundation of an emerging cellular Ser/Thr-kinase platform that involves a) coexpression of targeted kinases with promiscuous peptide substrates and b) quantification of intracellular substrate phosphorylation by homogeneous TR-FRET. Proof-of-concept data is provided for cellular AKT, B-RAF and CamK2delta assays. Importantly, comparable activity profiles were found for well characterized B-Raf inhibitors in TR-FRET assays relying on either promiscuous peptide substrates or a MEK1(WT) protein substrate respectively. Moreover, IC(50)-values correlated strongly between cellular TR-FRET assays and a gold standard Ba/F3 proliferation assay for B-Raf activity. Finally, we expanded our initial assay panel by screening a kinase-focused cDNA library and identified starting points for >20 cellular Ser/Thr-kinase assays.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"1 ","pages":"54-64"},"PeriodicalIF":0.0,"publicationDate":"2008-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28717913","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 a HTRF kinase assay for determination of Syk activity.","authors":"Christopher Harbert,&nbsp;Jeannette Marshall,&nbsp;Sharon Soh,&nbsp;Krista Steger","doi":"10.2174/1875397300801010020","DOIUrl":"https://doi.org/10.2174/1875397300801010020","url":null,"abstract":"<p><p>Regulation of protein phosphorylation is a primary cellular signaling mechanism. Many cellular responses to internal and external events are mitigated by protein kinase signaling cascades. Dysfunction of protein kinase activity has been linked to a variety of human pathologies, in the areas of cancer, inflammation, metabolism, cell cycle, apoptosis, as well as cardiovascular, neurodegenerative and autoimmune diseases. As such, there is an important need for protein kinase activity detection methodologies for researchers engaged in Drug Discovery. A number of different technologies have been employed for the measurement of protein kinase activity, including radioactive methods, luminescent methods, and fluorescent methods. More recently, Homogeneous Time Resolved Fluorescence technology (HTRF), based on the principle of time-resolved fluorescent resonance energy transfer (TR-FRET), has been developed and applied for the measurement of protein kinase activity in vitro. This technology note describes the development of an HTRF assay for detection of Syk enzyme activity in a format consistent with the requirements of High-Throughput Screening (HTS) campaigns currently used in drug discovery.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"1 ","pages":"20-6"},"PeriodicalIF":0.0,"publicationDate":"2008-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2174/1875397300801010020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28717997","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}