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1.  Artificial Neural Network Based Analysis of High Throughput Screening Data for Improved Prediction of Active Compounds 
Journal of biomolecular screening  2009;14(10):1236-1244.
Artificial Neural Networks (ANNs) are trained using High Throughput Screening (HTS) data to recover active compounds from a large data set. Improved classification performance was obtained on combining predictions made by multiple ANNs. The HTS data, acquired from a Methionine Aminopeptidases Inhibition study, consisted of a library of 43,347 compounds, and the ratio of active to non-active compounds, RA/N, was 0.0321. Back-propagation ANNs were trained and validated using Principal Components derived from the physico-chemical features of the compounds. On selecting the training parameters carefully, an ANN recovers one-third of all active compounds from the validation set with a three-fold gain in RA/N value. Further gains in RA/N values were obtained upon combining the predictions made by a number of ANNs. The generalization property of the back-propagation ANNs was utilized to train those ANNs with the same training samples, after being initialized with different sets of random weights. As a result, only 10% of all available compounds were needed for training and validation, and the rest of the data set was screened with more than a ten-fold gain of the original RA/N value. Thus, ANNs trained with limited HTS data might become useful in recovering active compounds from large data sets.
doi:10.1177/1087057109351312
PMCID: PMC4080791  PMID: 19940083
pattern classification; neural networks; generalization property
2.  Analysis of toxin induced changes in action potential shape for drug development 
Journal of biomolecular screening  2009;14(10):10.1177/1087057109348378.
The generation of an action potential is a complex process in excitable cells which involves the temporal opening and closing of several voltage-dependent ion channels in the cell membrane. The shape of an action potential can carry information concerning the state of the involved ion channels and their relationship to cellular processes. Alteration of these ion channels by the administration of toxins, drugs, and biochemicals can change the action potential’s shape in a specific way which can be characteristic for a given compound. Thus, action potential shape analysis could be a valuable tool to classify toxins and measure drug effects based on their mechanism of action. In an effort to begin classifying the effect of toxins on the shape of intracellularly recorded action potentials, patch clamp experiments were performed on NG108-15 hybrid cells in the presence of Veratridine, TEA, and quinine. To analyze the effect a computer model of the action potential mechanism was generated to determine to what extent each ion channel was affected during administration of these compounds based on the changes in the model parameters. Our work is a first step towards establishing a new assay system to detect and identify toxins by action potential shape analysis.
doi:10.1177/1087057109348378
PMCID: PMC3829631  PMID: 19801532
high-throughput; toxicity; cell models; electrophysiology; mechanisms
3.  Can phage display be used as a tool to functionally identify endogenous eat-me signals in phagocytosis? 
Journal of biomolecular screening  2009;14(6):10.1177/1087057109335679.
Removal of apoptotic cells and cellular debris by phagocytosis is essential for development, tissue homeostasis and resolution of inflammation. Eat-me signals control the initiation of phagocytosis, holding a key to our understanding of phagocyte biology. Due to lack of functional cloning strategy, eat-me signals are conventionally identified and characterized on a case-by-case basis. To investigate the feasibility of functionally cloning eat-me signals by phage display, we characterize the biological behavior of T7 phages displaying two well-known eat-me signals: growth arrest-specific gene 6 (Gas6) and milk fat globule-EGF8 (MFG-E8). Gas6-phage binds to all three known Gas6 receptors, Mer, Axl and Tyro3 receptor tyrosine kinases. Gas6-phage and MFG-E8-phage are capable of binding to phagocytes and non-phagocytes. However, both phages stimulate phage uptake only in phagocytes, including macrophages, microglia and retinal pigment epithelium (RPE) cells, but not in non-phagocytes. Furthermore, functional phage selection by phagocytosis in phagocytes enriches both Gas6-phage and MFG-E8-phage, suggesting that phage display can be used as a tool to functionally identify unknown eat-me signals from phage display cDNA library.
doi:10.1177/1087057109335679
PMCID: PMC3816984  PMID: 19531662
Eat-me signals; phagocytosis; phage display; Gas6; MFG-E8
4.  Detection of Intracellular Granularity Induction in Prostate Cancer Cell Lines by Small Molecules Using the HyperCyt® High-Throughput Flow Cytometry System 
Journal of biomolecular screening  2009;14(6):596-609.
Prostate cancer is a leading cause of death among men due to the limited number of treatment strategies available for advanced disease. Discovery of effective chemotherapeutics involves the identification of agents that inhibit cancer cell growth. Increases in intracellular granularity have been observed during physiological processes that include senescence, apoptosis, and autophagy, making this phenotypic change a useful marker for identifying small molecules that induce cellular growth arrest or death. In this regard, epithelial-derived cancer cell lines appear uniquely susceptible to increased intracellular granularity following exposure to chemotherapeutics. We have established a novel flow cytometry approach that detects increases in side light scatter in response to morphological changes associated with intracellular granularity in the androgen-sensitive LNCaP and androgen-independent PC3 human prostate cancer cell lines. A cell-based assay was developed to screen for small molecule inducers of intracellular granularity using the HyperCyt® high-throughput flow cytometry platform. Validation was performed using the Prestwick Chemical Library, where known modulators of LNCaP intracellular granularity, such as testosterone, were identified. Nonandrogenic inducers of granularity were also detected. A further screen of ~25,000 small molecules led to the identification of a class of aryl-oxazoles that increased intracellular granularity in both cell lines, often leading to cell death. The most potent agents exhibited submicromolar efficacy in LNCaP and PC3 cells.
doi:10.1177/1087057109335671
PMCID: PMC3666167  PMID: 19470718
HyperCyt® high-throughput flow cytometry; small molecule screening; intracellular granularity; prostate cancer
5.  Live Cell Imaging of Caspase Activation for High Content Screening 
Journal of biomolecular screening  2009;14(8):956-969.
Caspases are central to the execution of programmed cell death and their activation constitutes the biochemical hallmark of apoptosis. In this article, we report the successful adaptation of a high content assay method utilizing the DEVD-NucView488™ fluorogenic substrate, and for the first time, we show caspase activation in live cells induced either by drugs or siRNA. The fluorogenic substrate was found to be non-toxic over an exposure period of several days; during which we demonstrate automated imaging and quantification of caspase activation of the same cell population as a function of time. Overexpression of the anti-apoptotic protein Bcl-XL, alone or in combination with the inhibitor Z-VAD-FMK, attenuated caspase activation in HeLa cells exposed to Doxorubicin, Etoposide or cell death siRNA. Our method was further validated against two well characterized NSCLC cell lines reported to be sensitive (H3255) or refractory (H2030) to Erlotinib; where we show a differential time dependent activation was observed for H3255 and no significant changes in H2030, consistent with their respective chemosensitivity profile. In summary, our results demonstrate the feasibility of using this newly adapted and validated high content assay to screen chemical or RNAi libraries for the identification of previously uncovered enhancers and suppressors of the apoptotic machinery in live cells.
doi:10.1177/1087057109343207
PMCID: PMC3613133  PMID: 19726787
High content assay; RNAi HT screening; Chemical HT screening; caspase; apoptosis; cancer; live cells
6.  Dose-Response Modeling of High-Throughput Screening Data 
Journal of biomolecular screening  2009;14(10):1216-1227.
The National Toxicology Program is developing a high throughput screening (HTS) program to set testing priorities for compounds of interest, to identify mechanisms of action, and potentially to develop predictive models for human toxicity. This program will generate extensive data on the activity of large numbers of chemicals in a wide variety of biochemical-and cell-based assays. The first step in relating patterns of response among batteries of HTS assays to in vivo toxicity is to distinguish between positive and negative compounds in individual assays. Here, we report on a statistical approach developed to identify compounds positive or negative in a HTS cytotoxicity assay based on data collected from screening 1353 compounds for concentration-response effects in nine human and four rodent cell types. In this approach, we develop methods to normalize the data (removing bias due to the location of the compound on the 1536-well plates used in the assay) and to analyze for concentration-response relationships. Various statistical tests for identifying significant concentration-response relationships and for addressing reproducibility are developed and presented.
doi:10.1177/1087057109349355
PMCID: PMC3471146  PMID: 19828774
high-throughput screening; dose-response; statistical modeling; viability assay
7.  Identification of a Small GTPase Inhibitor using a High-Throughput Flow Cytometry Bead-Based Multiplex Assay 
Small GTPases are key regulators of cellular activity and represent novel targets for the treatment of human diseases using small molecule inhibitors. We describe a multiplex, flow cytometry bead-based assay for the identification and characterization of inhibitors or activators of small GTPases. Six different GST-tagged small GTPases were bound to glutathione beads each labeled with a different red fluorescence intensity. Subsequently, beads bearing different GTPase were mixed and dispensed into 384-well plates with test compounds, and fluorescent-GTP binding was used as the read-out. This novel multiplex assay allowed us to screen a library of almost 200,000 compounds and identify over 1,200 positive compounds, which were further verified by dose response analyses, using 6 to 8-plex assays. After the elimination of false positive and negative compounds, several small molecule families with opposing effects on GTP-binding activity were identified. Here we detail the characterization of MLS000532223, a general inhibitor that prevents GTP-binding to several GTPases in a dose-dependent manner and is active in biochemical and cell-based secondary assays. Live cell imaging and confocal microscopy studies revealed the inhibitor-induced actin reorganization and cell morphology changes, characteristic of Rho GTPases inhibition. Thus, high throughput screening (HTS) via flow cytometry provides a strategy for identifying novel compounds that are active against small GTPases.
doi:10.1177/1087057109352240
PMCID: PMC3433230  PMID: 20008126
Ras; Rab and Rho GTPases; actin cytoskeleton; bead-based multiplex assay; flow cytometry; fluorescent GTP binding
8.  Monitoring compound integrity with cytochrome P450 assays and qHTS 
Journal of biomolecular screening  2009;14(5):538-546.
We describe how room temperature storage of a 1,120 member compound library prepared in either DMSO or in a hydrated DMSO/water (67/33) mixture affects the reproducibility of potency values as monitored using cytochrome P450 1A2 and 2D6 isozyme assays. The bioluminescent assays showed Z′-factors of 0.71 and 0.62, with 18% and 32% of the library found as active against the CYP 1A2 and 2D6 isozymes respectively. We tested the library using quantitative high-throughput screening to generate potency values for every library member which was measured at seven time intervals spanning 37 weeks. We calculated the minimum significant ratio (MSR) from these potency values at each time interval and we found that for the library stored in DMSO, the CYP 1A2 and 2D6 assay MSRs progressed from approximately 2.0 to 5.0. The hydrated conditions showed similar performance in both MSR progression and analytical QC results. Based on this study we recommend that DMSO samples be stored in 1,536-well plates for < 4 months at room temperature. Further, the study shows the magnitude of potency changes that can occur in a robust bioassay due to compound sample storage.
doi:10.1177/1087057109336954
PMCID: PMC3430136  PMID: 19483146
HTS; compound storage; DMSO; quantitative HTS
9.  Identification and Characterization of Novel Tissue-Nonspecific Alkaline Phosphatase Inhibitors with Diverse Modes of Action 
Journal of Biomolecular Screening  2009;14(7):824-837.
Tissue-nonspecific alkaline phosphatase (TNAP) plays a major role in maintaining a ratio of phosphate to inorganic pyrophosphate (Pi/PPi) in biological fluids that is conducive to controlled skeletal mineralization while preventing inappropriate ectopic calcification. Medial calcification associated with Enpp1 or Ank deficiency or with end–stage renal disease is associated with an increase in TNAP activity in arteries that leads to reduced levels of PPi and increased vascular calcification. Here, we describe in detail a high-throughput screening (HTS) campaign to identify inhibitors of TNAP, performed within the Molecular Library Screening Center Network (MLSCN). A homogeneous luminescent TNAP assay was developed and optimized for identification of compounds with diverse mechanism of action (MOA). The MLSCN compound collection, containing 64,394 molecules at the time of screening, was tested in the assay. Several novel inhibitory scaffold classes were identified and demonstrated to have diverse selectivity and mode of inhibition (MOI) profiles. Representatives of the novel scaffolds exhibited nanomolar potency surpassing the inhibitors known to date.
This paper sets a successful example in which pharmacologically active compounds, with outstanding selectivity in a panel of more than 200 assays, are identified from high throughput screening. Integral to the success of the project were a well-designed compound collection, an industrial-level screening facility and a deep knowledge of target biology that were brought together through the NIH-sponsored Roadmap Initiative.
doi:10.1177/1087057109338517
PMCID: PMC3403534  PMID: 19556612
NIH Roadmap Initiatives; MLSCN; TNAP inhibitors; diverse MOA; compound selectivity
10.  Virtual Screening Against α-Cobratoxin 
Journal of biomolecular screening  2009;14(9):1109-1118.
α-Cobratoxin (Cbtx), the neurotoxin isolated from the venom of the Thai cobra Naja kaouthia, causes paralysis by preventing acetylcholine (ACh) binding to nicotinic acetylcholine receptors (nAChRs). In the current study, the region of the Cbtx molecule that is directly involved in binding to nAChRs is used as the target for anticobratoxin drug design. The crystal structure (1YI5) of Cbtx in complex with the acetylcholine binding protein (AChBP), a soluble homolog of the extracellular binding domain of nAChRs, was selected to prepare an α-cobratoxin active binding site for docking. The amino acid residues (Ser182-Tyr192) of the AChBP structure, the binding site of Cbtx, were used as the positive control to validate the prepared Cbtx active binding site (root mean square deviation < 1.2 Å). Virtual screening of the National Cancer Institute diversity set, a library of 1990 compounds with nonredundant pharmacophore profiles, using AutoDock against the Cbtx active site, revealed 39 potential inhibitor candidates. The adapted in vitro radioligand competition assays using [3H]epibatidine and [125I]bungarotoxin against the AChBPs from the marine species, Aplysia californica (Ac), and from the freshwater snails, Lymnaea stagnalis (Ls) and Bolinus truncates (Bt), revealed 4 compounds from the list of inhibitor candidates that had micromolar to nanomolar interferences for the toxin binding to AChBPs. Three hits (NSC42258, NSC121865, and NSC134754) can prolong the survival time of the mice if administered 30 min before injection with Cbtx, but only NSC121865 and NSC134754 can prolong the survival time if injected immediately after injection with Cbtx. These inhibitors serve as novel templates/scaffolds for the development of more potent and specific anticobratoxin.
doi:10.1177/1087057109344617
PMCID: PMC3191909  PMID: 19734437
α-cobratoxin; virtual screening; docking; neurotoxin; nicotinic acetylcholine receptor
11.  Identification and preliminary characterization of novel small molecules that inhibit growth of human lung adenocarcinoma cells 
Journal of biomolecular screening  2009;14(10):1176-1184.
Drug treatment for human lung cancers remains unsatisfactory, despite the identification of many potential therapeutic targets (such as mutant KRAS protein) and the approval of agents that inhibit the tyrosine kinase activity of mutant epidermal growth factor receptor (EGFR). To seek new therapeutic strategies against lung tumors, we have screened 189, 290 small molecules for their ability to retard growth of human lung adenocarcinoma cell lines, which harbor mutations in EGFR or KRAS. Four candidates that are structurally different from common tyrosine kinase inhibitors were selected for further study. We describe one small molecule (designated lung cancer screen-1, LCS-1) in detail here. Identification of the targets of LCS-1 and other growth inhibitors found in this screen may help to develop new agents for treatment of lung adenocarcinomas, including those driven by mutant EGFR and KRAS.
doi:10.1177/1087057109350919
PMCID: PMC3146390  PMID: 19887599
high throughput drug screen; lung cancer; EGFR; KRAS
12.  An AlphaScreen™ Based High-throughput Screen to Identify Inhibitors of Hsp90 and Cochaperone Interaction 
Journal of biomolecular screening  2009;14(3):273-281.
Hsp90 has emerged as an important anti-cancer drug target because of its essential role in promoting the folding and maturation of many oncogenic proteins. Here we describe the development of the first high throughput screen, based on AlphaScreen™ technology, to identify a novel type of Hsp90 inhibitors that interrupt its interaction with the cochaperone HOP. The assay uses the 20-mer C-terminal peptide of Hsp90 and the TPR2A domain of HOP. Assay specificity was demonstrated by measuring different interactions using synthetic peptides, with measured IC50s in good agreement with reported values. The assay is stable over 12 hours and tolerates DMSO up to 5%. We first validated the assay by screening against 20,000 compounds in 384-well format. After further optimization into a 1536-well format, it was screened against a NCGC library of 76,134 compounds, with a signal-to-background (S/B) ratio of 78 and Z’ factor of 0.77. The present assay can be used for discovery of novel small molecule Hsp90 inhibitors that can be used as chemical probes to investigate the role of cochaperones in Hsp90 function. Such molecules have the potential to be developed into novel anti-cancer drugs, for use alone or in combination with other Hsp90 inhibitors.
doi:10.1177/1087057108330114
PMCID: PMC3066041  PMID: 19211782
heat shock protein 90 (Hsp90); Hsp organizing protein (HOP); tetratricopeptide repeat (TPR); AlphaScreen™; high-throughput screening (HTS)
13.  Development of a High-Throughput Cell-Based Reporter Assay to Identify Stabilizers of Tumor Suppressor Pdcd4 
The novel tumor suppressor Pdcd4 affects tumorigenesis by inhibiting translation. Pdcd4 is phosphorylated and subsequently lost by proteasomal degradation in response to tumor promoting conditions. Here, we describe the development of a reporter cell system to monitor the stability of Pdcd4. The phosphorylation-dependent degradation domain (“target”) or an adjacent (“off-target”) region of Pdcd4 were cloned into a luciferase expression system. The target constructs were responsive to Pdcd4 degrading conditions (e.g. TPA, p70S6K1-overactivation), while the off-target constructs remained stable. The system was optimized for and shown to be reliable in a high-throughput compatible 384-well format. Screening of 15,275 pure compounds resulted in a hit rate of 0.30% (> 50% inhibition of TPA-induced loss of signal, confirmed by re-assay). Among the hits were inhibitors of previously identified critical signaling events for TPA-induced Pdcd4 degradation. One compound was identified to be nonspecific using the off-target control cell line. Screening of 135,678 natural product extracts yielded 42 confirmed, specific hits. Z’ averaged 0.58 across 446 plates. Further characterization of active natural products and synthetic compounds is expected to identify novel Pdcd4 stabilizers that may be useful in targeting translation to prevent or treat cancers.
doi:10.1177/1087057109351028
PMCID: PMC2853809  PMID: 19901084
Pdcd4; translation; tumor suppressor; high-throughput assay; natural products
14.  Two Gαi1 Rate-Modifying Mutations Act in Concert to Allow Receptor-Independent, Steady-State Measurements of RGS Protein Activity 
Journal of biomolecular screening  2009;14(10):1195-1206.
RGS proteins are critical modulators of G protein-coupled receptor (GPCR) signaling given their ability to deactivate Gα subunits via “GTPase-accelerating protein” (GAP) activity. Their selectivity for specific GPCRs makes them attractive therapeutic targets. However, measuring GAP activity is complicated by slow GDP release from Gα and lack of solution-phase assays for detecting free GDP in the presence of excess GTP. To overcome these hurdles, we developed a Gαi1 mutant with increased GDP dissociation and decreased GTP hydrolysis, enabling detection of GAP activity using steady-state GTP hydrolysis. Gαi1(R178M/A326S) GTPase activity was stimulated 6~12 fold by RGS proteins known to act on Gαi subunits, and not affected by those unable to act on Gαi, demonstrating that the Gα/RGS domain interaction selectivity was not altered by mutation. Gαi1(R178M/A326S) interacted with RGS proteins with expected binding specificity and affinities. To enable non-radioactive, homogenous detection of RGS protein effects on Gαi1(R178M/A326S), we developed a Transcreener® fluorescence polarization immunoassay based on a monoclonal antibody that recognizes GDP with greater than 100-fold selectivity over GTP. Combining Gαi1(R178M/A326S) with a homogenous, fluorescence-based GDP detection assay provides a facile means to explore the targeting of RGS proteins as a new approach for selective modulation of GPCR signaling.
doi:10.1177/1087057109347473
PMCID: PMC2795102  PMID: 19820068
Fluorescence polarization; GDP detection; regulators of G-protein signaling; surface plasmon resonance
15.  Inhibitors of RecA Activity Discovered by High-Throughput Screening: Cell-Permeable Small Molecules Attenuate the SOS Response in Escherichia coli 
Journal of biomolecular screening  2009;14(9):1092-1101.
The phenomenon of antibiotic resistance has created a need for the development of novel antibiotic classes with non-classical cellular targets. Unfortunately, target-based drug discovery against proteins considered essential for in vitro bacterial viability has yielded few new therapeutic classes of antibiotics. Targeting the large proportion of genes considered nonessential that have yet to be explored by HTS, e.g., RecA, can complement these efforts. Recent evidence suggests that RecA-controlled processes are responsible for tolerance to antibiotic chemotherapy and are involved in pathways that ultimately lead to full-fledged antibiotic resistance. Therefore inhibitors of RecA may serve as therapeutic adjuvants in combination chemotherapy of bacterial infectious diseases. Towards the goal of validating RecA as a novel target in the chemotherapy of bacterial infections, we have screened 35,780 small molecules against RecA. In total, 80 small molecules were identified as primary hits and could be clustered in six distinct chemotype clades. The most potent class of hits was further examined, and one member compound was found to inhibit RecA-mediated strand exchange and prevent ciprofloxacin-induced SOS expression in Escherichia coli. This compound represents the first small molecule demonstrating an ability to inhibit the bacterial SOS response in live bacterial cell cultures.
doi:10.1177/1087057109342126
PMCID: PMC2877376  PMID: 19675313
RecA; antibiotic resistance; ATPase inhibition; ciprofloxacin; SOS response
16.  A High-Throughput Method to Identify Novel Senescence-Inducing Compounds 
Journal of biomolecular screening  2009;14(7):853-858.
Cellular senescence is a persistently growth-arrested phenotype in normal and transformed cells induced by non-cytotoxic stress. Cytostasis as a method of cancer treatment has recently generated significant interest. Research into the induction of cellular senescence as cancer therapy has been hindered by a lack of compounds that efficiently induce this response. We describe a semiautomated high-throughput method to identify library compounds that induce senescence using prostate cancer cells cultured in 96 well plates. Primary hits are identified by low cell numbers after 3 days in culture, measured by Hoechst 33342 fluorescence. A secondary visual assessment of senescence-associated β-galactosidase staining and cellular morphology in the same wells distinguishes senescence from quiescence, apoptosis and other false-positives. This method was used to screen a 4160 compound library of known bioactive compounds and natural products at a 10μM dose. Candidate compounds were further selected based on persistent growth arrest after drug removal and increased expression of previously described senescence marker genes. Four lead compounds not previously associated with senescence were identified for further investigation. This is the first successful assay to identify novel agents from compound libraries based on senescence-induction in cancer cells.
doi:10.1177/1087057109340314
PMCID: PMC2913693  PMID: 19641224
cellular senescence; high-throughput screen; prostate; prostate cancer
17.  Polyplexed FCPIA (Flow Cytometry Protein Interaction Assay): A Novel High Throughput Screening Paradigm For RGS Protein Inhibitors 
Journal of biomolecular screening  2009;14(6):610-619.
Intracellular signaling cascades are a series of regulated protein-protein interactions that may provide a number of targets for potential drug discovery. Here, we examine the interaction of Regulators of G protein signaling (RGS) proteins with the G protein Gαo, using a flow cytometry protein interaction assay (FCPIA). FCPIA accurately measures nanomolar binding constants of this protein-protein interaction, and has been used in high throughput screening. This report focuses on five RGS proteins (4, 6, 7, 8 and 16). In order to increase the content of screens, we assessed high throughput screening of these RGS proteins in multiplex, by establishing binding constants of each RGS with Gαo in isolation, and then in a multiplex format with five RGS proteins present. In order to use this methodology as a higher-content multiplex protein-protein interaction screen, we established Z' factor values for RGS proteins in multiplex of 0.73 to 0.92, indicating this method is suitable for screening using FCPIA. To increase throughput, we also compressed a set of 8,000 compounds by combining 4 compounds in a single assay well. Subsequent deconvolution of the compounds mixtures verified the identification of active compounds at specific RGS targets in our mixtures using the polyplexed FCPIA method.
doi:10.1177/1087057109336590
PMCID: PMC2908316  PMID: 19531661
G protein; RGS; Flow Cytometry; FCPIA; High throughput screening
18.  Maximizing RNA yield from archival renal tumors and optimizing gene expression analysis 
Formalin-fixed paraffin-embedded tissues are widely available for gene expression analysis using TaqMan PCR. Five methods, including 4 commercial kits, for recovering RNA from paraffin embedded renal tumor tissue were compared. The MasterPure kit from Epicentre produced the highest RNA yield. However, the difference in RNA yield between the kit from Epicenter and Invitrogen’s Trizol method was not significant. Using the top 3 RNA isolation methods, the manufacturers’ protocols were modified to include an overnight Proteinase K digestion. Overnight protein digestion resulted in significant increase in RNA yield. To improve cDNA production by reverse transcription, random oligonucleotide primers were compared to gene-specific primers targeting the genes of interest. Reverse transcription using gene-specific primers significantly increased the quantity of cDNA detectable by TaqMan PCR. Therefore, expression profiling of formalin-fixed paraffin-embedded tissue using TaqMan qPCR can be optimized by using the Masterpure RNA isolation kit modified to include an overnight proteinase K digestion and gene-specific primers during the reverse transcription.
doi:10.1177/1087057109355059
PMCID: PMC2902272  PMID: 20008123
formalin-fixed paraffin-embedded; RNA; TaqMan qPCR
19.  Dequalinium, a New Inhibitor of Mycobacterium tuberculosis Mycothiol Ligase Identified by High-Throughput Screening 
Journal of biomolecular screening  2009;14(6):643-652.
Mycothiol ligase (MshC) is a key enzyme in the biosynthesis of mycothiol, a small molecular weight thiol that is unique to actinomycetes and whose primary role is to maintain intracellular redox balance and remove toxins. MshC catalyzes the adenosine triphosphate (AT P)–dependent condensation of cysteine and glucosamine-inositol (GI) to produce cysteine-glucosamine-inositol (CGI). MshC is essential to Mycobacterium tuberculosis and therefore represents an attractive target for chemotherapeutic intervention. A screening protocol was developed to identify MshC inhibitors based on quantification of residual ATP using a coupled luminescent assay. The protocol was used to screen a library of 3100 compounds in a 384- well plate format (Z′ ≥ 0.65). Fifteen hits (0.48%) were identified from the screen, and 2 hits were confirmed in a secondary assay that measures production of CGI. The structures of both hits contain N-substituted quinolinium moieties, and the more potent of the 2—namely, dequalinium chloride—inhibits MshC with an IC50 value of 24 ± 1 μM. Further studies showed dequalinium to be an AT P-competitive inhibitor of MshC, to bind MshC with a KD of 0.22 μM, and to inhibit the growth of M. tuberculosis under aerobic and anaerobic conditions with minimum inhibitory and anaerobic bactericidal concentrations of 1.2 and 0.3 μg/mL, respectively. The screening protocol described is robust and has enabled the identification of new MshC inhibitors.
doi:10.1177/1087057109335743
PMCID: PMC2796824  PMID: 19525487
competitive inhibitor; luminescent assay; mycothiol biosynthesis; screening; small molecular weight thiol
20.  Buffer Optimization of Thermal Melt Assays of Plasmodium Proteins for Detection of Small-Molecule Ligands 
Journal of biomolecular screening  2009;14(6):700-707.
In the last decade, thermal melt/thermal shift assays have become a common tool for identifying ligands and other factors that stabilize specific proteins. Increased stability is indicated by an increase in the protein's melting temperature (Tm). In optimizing the assays for subsequent screening of compound libraries, it is important to minimize the variability of Tm measurements so as to maximize the assay's ability to detect potential ligands. Here we present an investigation of Tm variability in recombinant proteins from Plasmodium parasites. Ligands of Plasmodium proteins are particularly interesting as potential starting points for drugs for malaria, and new drugs are urgently needed. A single standard buffer (100 mM HEPES, pH 7.5, 150 mM NaCl) permitted estimation of Tm for 58 of 61 Plasmodium proteins tested. However, with several proteins, Tm could not be measured with a consistency suitable for high-throughput screening unless alternative protein-specific buffers were employed. We conclude that buffer optimization to minimize variability in Tm measurements increases the success of thermal melt screens involving proteins for which a standard buffer is suboptimal.
doi:10.1177/1087057109335749
PMCID: PMC2819745  PMID: 19470714
thermal shift assays; protein unfolding; protein stabilization; superoxide dismutase
21.  Automated High-Content Screening for Compounds That Disassemble the Perinucleolar Compartment 
Journal of biomolecular screening  2009;14(9):1045-1053.
All solid malignancies share characteristic traits, including unlimited cellular proliferation, evasion of immune regulation, and the propensity to metastasize. The authors have previously described that a subnuclear structure, the perinucleolar compartment (PNC), is associated with the metastatic phenotype in solid tumor cancer cells. The percentage of cancer cells that contain PNCs (PNC prevalence) is indicative of the malignancy of a tumor both in vitro and in vivo, and thus PNC prevalence is a marker that reflects metastatic capability in a population of tumor cells. Although the function of the PNC remains to be determined, the PNC is highly enriched with small RNAs and RNA binding proteins. The initial chemical biology studies using a set of anticancer drugs that disassemble PNCs revealed a direct association of the structure with DNA. Therefore, PNC prevalence reduction as a phenotypic marker can be used to identify compounds that target cellular processes required for PNC maintenance and hence used to elucidate the nature of the PNC function. Here the authors report the development of an automated high-content screening assay that is capable of detecting PNC prevalence in prostate cancer cells (PC-3M) stably expressing a green fluorescent protein (GFP)–fusion protein that localizes to the PNC. The assay was optimized using known PNC-reducing drugs and non-PNC-reducing cytotoxic drugs. After optimization, the fidelity of the assay was probed with a collection of 8284 compounds and was shown to be robust and capable of detecting known and novel PNC-reducing compounds, making it the first reported high-content phenotypic screen for small changes in nuclear structure.
doi:10.1177/1087057109343120
PMCID: PMC2857721  PMID: 19762548
high-content screening; nucleus; cancer; perinucleolar compartment; small molecules
22.  A Set of Time-Resolved Fluorescence Resonance Energy Transfer Assays for the Discovery of Inhibitors of Estrogen Receptor-Coactivator Binding 
Journal of biomolecular screening  2009;14(2):181-193.
Therapeutic block of estrogen action is typically achieved with conventional antagonists (CAs), compounds that displace estradiol from the estrogen receptor (ER) and induce formation of an ER conformation that cannot bind to coactivator proteins, such as the steroid receptor coactivators (SRCs). As an alternative mode for blocking estrogen action, we are seeking small molecules that act as coactivator binding inhibitors (CBIs), i.e., they compete directly with SRC3 for interaction with estradiol-bound ER. CBIs would be interesting mechanistic probes of estrogen action and might also provide an alternative, more durable endocrine therapy for hormone-responsive breast cancer, where cellular adaptations lead to resistance to CAs. We have designed and optimized a set of time-resolved fluorescence resonance energy transfer (TR-FRET) assays to monitor the interaction of ER with SRC3 and ligands, and we have used them in high-throughput screens to discover small molecule CBIs that are able to disrupt this interaction. These assays also distinguish CBIs from CAs. These robust and sensitive “mix and measure” assays use low concentrations of ER labeled with a europium chelate as FRET donor and a Cy5-labeled SRC as acceptor. This multiplexed protocol produces excellent signal to noise ratios (> 100) and Z' values (> 0.8).
doi:10.1177/1087057108329349
PMCID: PMC2731238  PMID: 19196699
23.  High-Throughput Screening for Small Molecule Inhibitors of LARG-Stimulated RhoA Nucleotide Binding via a Novel Fluorescence Polarization Assay 
Journal of biomolecular screening  2009;14(2):161-172.
Guanine nucleotide-exchange factors (GEFs) stimulate guanine nucleotide exchange and the subsequent activation of Rho-family proteins in response to extracellular stimuli acting upon cytokine, tyrosine kinase, adhesion, integrin, and G-protein coupled receptors (GPCRs). Upon Rho activation, several downstream events occur, such as morphological and cytokskeletal changes, motility, growth, survival, and gene transcription. The RhoGEF Leukemia-Associated RhoGEF (LARG) is a member of the Regulators of G-protein Signaling Homology Domain (RH) family of GEFs originally identified as a result of chromosomal translocation in acute myeloid leukemia. Using a novel fluorescence polarization guanine nucleotide binding assay utilizing BODIPY-Texas Red-GTPγS (BODIPY-TR-GTPγS), we performed a ten-thousand compound high-throughput screen for inhibitors of LARG-stimulated RhoA nucleotide binding. Five compounds identified from the high-throughput screen were confirmed in a non-fluorescent radioactive guanine nucleotide binding assay measuring LARG-stimulated [35S] GTPγS binding to RhoA, thus ruling out non-specific fluorescent effects. All five compounds selectively inhibited LARG-stimulated RhoA [35S] GTPγS binding, but had little to no effect upon RhoA or Gαo [35S] GTPγS binding. Therefore, these five compounds should serve as promising starting points for the development of small molecule inhibitors of LARG-mediated nucleotide exchange as both pharmacological tools and therapeutics. In addition, the fluorescence polarization guanine nucleotide binding assay described here should serve as a useful approach for both high-throughput screening and general biological applications.
doi:10.1177/1087057108328761
PMCID: PMC2698131  PMID: 19196702
high-throughput screening; fluorescence polarization; RhoGEF; RhoA; LARG; Drug Discovery
24.  A High-Throughput Ligand Competition Binding Assay for the Androgen Receptor and other Nuclear Receptors 
Standardized, automated ligand binding assays facilitate evaluation of endocrine activities of environmental chemicals and identification of antagonists of nuclear receptor ligands. Many current assays rely on fluorescently labeled ligands which are significantly different from the native ligands. We describe a radiolabeled ligand competition scintillation proximity assay (SPA) for the androgen receptor (AR) using Ni-coated 384-well FlashPlates® and liganded AR-LBD protein. This highly reproducible, low cost assay is well-suited for automated HTS. Additionally, we show that this assay can be adapted to measure ligand affinities for other nuclear receptors (peroxisome proliferation activated receptor γ, thyroid receptors α and β).
doi:10.1177/1087057108326662
PMCID: PMC2632761  PMID: 19171919
Scintillation Proximity Assay; androgen receptor; high-throughput screening; endocrine disrupting chemicals; nuclear receptors

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