Recent Publications:

Nature Biotechnology	Comprehensive characterization of cytochrome P450 isozyme selectivity across chemical libraries [ PDF ] Veith H, Southall N, Huang R, James T, Fayne D, Artemenko N, Shen M, Inglese J, Austin CP, Lloyd DG, Auld DS The cytochrome P450 (CYP) gene family catalyzes drug metabolism and bioactivation and is therefore relevant to drug development. We determined potency values for 17,143 compounds against five recombinant CYP isozymes (1A2, 2C9, 2C19, 2D6 and 3A4) using an in vitro bioluminescent assay. The compounds included libraries of US Food and Drug Administration (FDA)-approved drugs and screening libraries. We observed cross-library isozyme inhibition (30–78%) with important differences between libraries. Whereas only 7% of the typical screening library was inactive against all five isozymes, 33% of FDA-approved drugs were inactive, reflecting the optimized pharmacological properties of the latter. Our results suggest that low CYP 2C isozyme activity is a common property of drugs, whereas other isozymes, such as CYP 2D6, show little discrimination between drugs and unoptimized compounds found in screening libraries. We also identified chemical substructures that differentiated between the five isozymes. The pharmacological compendium described here should further the understanding of CYP isozymes.
Current Topics in Medicinal Chemistry	The Pilot Phase of the NIH Chemical Genomics Center. [ PDF ] Thomas CJ, Auld DS, Huang R, Huang W, Jadhav A, Johnson RL, Leister W, Maloney DJ, Marugan JJ, Michael S, Simeonov A, Southall N, Xia M, Zheng W, Inglese J, Austin CP. The NIH Chemical Genomics Center (NCGC) was the inaugural center of the Molecular Libraries and Screening Center Network (MLSCN). Along with the nine other research centers of the MLSCN, the NCGC was established with a primary goal of bringing industrial technology and experience to empower the scientific community with small molecule compounds for use in their research. We intend this review to serve as 1) an introduction to the NCGC standard operating procedures, 2) an overview of several of the lessons learned during the pilot phase and 3) a review of several of the innovative discoveries reported during the pilot phase of the MLSCN.
Toxicological Sciences	Weighted Feature Significance (WFS): A Simple, Interpretable Model of Compound Toxicity Based on the Statistical Enrichment of Structural Features. [ PDF ] Huang R, Southall N, Xia M, Cho MH, Jadhav A, Nguyen DT, Inglese J, Tice RR, Austin CP In support of the U.S. Tox21 program, we have developed a simple and chemically intuitive model we call Weighted Feature Significance (WFS) to predict the toxicological activity of compounds, based on the statistical enrichment of structural features in toxic compounds. We trained and tested the model on: (1) data from quantitative high-throughput screening (qHTS) cytotoxicity and caspase activation assays conducted at the NIH Chemical Genomics Center (NCGC), (2) data from Salmonella typhimurium reverse mutagenicity assays conducted by the U.S. National Toxicology Program (NTP), and (3) hepatotoxicity data published in the Registry of Toxic Effects of Chemical Substances (RTECS). Enrichments of structural features in toxic compounds are evaluated for their statistical significance and compiled into a simple additive model of toxicity, and then used to score new compounds for potential toxicity. The predictive power of the model for cytotoxicity was validated using an independent set of compounds from the U.S. Environmental Protection Agency (EPA) tested also at the NCGC. We compared the performance of our WFS approach with classical classification methods such as Naïve Bayesian clustering and support vector machines. In most test cases, WFS showed similar or slightly better predictive power, especially in the prediction of hepatotoxic compounds, where WFS appeared to have the best performance among the three methods. The new algorithm has the important advantages of simplicity, power, interpretability, and ease of implementation.
Camcer Research	Cardiac glycosides inhibit p53 synthesis by a mechanism relieved by Src or MAPK inhibition. [ PDF ] Wang Z, Zheng M, Li Z, Li R, Jia L, Xiong X, Southall N, Wang S, Xia M, Austin CP, Zheng W, Xie Z, Sun Y. p53 is regulated at multiple levels. We report here that p53, in multiple lines of human cancer cells, is down-regulated by cardiac glycoside drugs digoxin and ouabain, potent inhibitors of Na(+)/K(+)-ATPase. These drugs reduced the basal levels of p53 protein at nanomolar concentrations in a dose-, time-, and cancer cell line-dependent manner, but independent of p53 status of wild-type or mutant. The drugs also reduced the levels of p53 induced by its activators as well as p53 transfected into human cancer cells, regardless of its status. Interestingly, the drugs had no effect on endogenous p53 in two immortalized human cell lines. Mechanistically, p53 reduction occurred not at the mRNA levels but at the protein levels, as a result of reduced protein synthesis rather than enhanced degradation. The cellular sensitivity to drug-induced p53 reduction was not associated with the levels of alphasubunits of Na(+)/K(+)-ATPase in different cell lines. Although lowering extracellular K(+) did not reduce p53 as did ouabain and digoxin, it did potentiate both digoxin- and ouabain-induced p53 reduction in sensitive lines. Finally, p53 reduction seems to be triggered by activation of Src/mitogen-activated protein kinase (MAPK) signaling pathways upon drug binding to the Na(+)/K(+)-ATPase and can be completely blocked by the inhibitors of Src or MAP/ERK kinase. This is the first report that cardiac glycoside drugs, by initiating the Src/MAPK signaling pathways, reduce the p53 levels via inhibition of p53 protein synthesis. The drugs may be useful in the treatment of human cancers with a gain-of-function p53 mutation.
Proceedings of the National Academy of Sciences	Small-molecule agonists for the thyrotropin receptor stimulate thyroid function in human thyrocytes and mice. [ PDF ] Neumann S, Huang W, Titus S, Krause G, Kleinau G, Alberobello AT, Zheng W, Southall NT, Inglese J, Austin CP, Celi FS, Gavrilova O, Thomas CJ, Raaka BM, Gershengorn MC. Seven-transmembrane-spanning receptors (7TMRs) are prominent drug targets. However, small-molecule ligands for 7-transmembrane-spanning receptors for which the natural ligands are large, heterodimeric glycoprotein hormones, like thyroid-stimulating hormone (TSH; thyrotropin), have only recently been reported, and none are approved for human use. We have used quantitative high-throughput screening to identify a small-molecule TSH receptor (TSHR) agonist that was modified to produce a second agonist with increased potency. We show that these agonists are highly selective for human TSHR versus other glycoprotein hormone receptors and interact with the receptor's serpentine domain. A binding pocket within the transmembrane domain was defined by docking into a TSHR homology model and was supported by site-directed mutagenesis. In primary cultures of human thyrocytes, both TSH and the agonists increase mRNA levels for thyroglobulin, thyroperoxidase, sodium iodide symporter, and deiodinase type 2, and deiodinase type 2 enzyme activity. Moreover, oral administration of the agonist stimulated thyroid function in mice, resulting in increased serum thyroxine and thyroidal radioiodide uptake. Thus, we discovered a small molecule that activates human TSHR in vitro, is orally active in mice, and could be a lead for development of drugs to use in place of recombinant human TSH in patients with thyroid cancer.
Molecular Biosystems	A quantitative high-throughput screen for modulators of IL-6 signaling: a model for interrogating biological networks using chemical libraries. [ PDF ] Johnson RL, Huang R, Jadhav A, Southall N, Wichterman J, MacArthur R, Xia M, Bi K, Printen J, Austin CP, Inglese J. Small molecule modulators are critical for dissecting and understanding signaling pathways at the molecular level. Interleukin 6 (IL-6) is a cytokine that signals via the JAK-STAT pathway and is implicated in cancer and inflammation. To identify modulators of this pathway, we screened a chemical collection against an IL-6 responsive cell line stably expressing a beta-lactamase reporter gene fused to a sis-inducible element (SIE-bla cells). This assay was optimized for a 1536-well microplate format and screened against 11 693 small molecules using quantitative high-throughput screening (qHTS), a method that assays a chemical library at multiple concentrations to generate titration-response profiles for each compound. The qHTS recovered 564 actives with well-fit curves that clustered into 32 distinct chemical series of 13 activators and 19 inhibitors. A retrospective analysis of the qHTS data indicated that single concentration data at 1.5 and 7.7 microM scored 35 and 71% of qHTS actives, respectively, as inactive and were therefore false negatives. Following counter screens to identify fluorescent and non-selective series, we found four activator and one inhibitor series that modulated SIE-bla cells but did not show similar activity in reporter gene assays induced by EGF and hypoxia. Small molecules within these series will make useful tool compounds to investigate IL-6 signaling mediated by JAK-STAT activation.
Analytical Biochemistry	A new homogeneous high-throughput screening assay for profiling compound activity on the human ether-a-go-go-related gene channel. [ PDF ] Titus SA, Beacham D, Shahane SA, Southall N, Xia M, Huang R, Hooten E, Zhao Y, Shou L, Austin CP, Zheng W. Long QT syndrome, either inherited or acquired from drug treatments, can result in ventricular arrhythmia (torsade de pointes) and sudden death. Human ether-a-go-go-related gene (hERG) channel inhibition by drugs is now recognized as a common reason for the acquired form of long QT syndrome. It has been reported that more than 100 known drugs inhibit the activity of the hERG channel. Since 1997, several drugs have been withdrawn from the market due to the long QT syndrome caused by hERG inhibition. Food and Drug Administration regulations now require safety data on hERG channels for investigative new drug (IND) applications. The assessment of compound activity on the hERG channel has now become an important part of the safety evaluation in the process of drug discovery. During the past decade, several in vitro assay methods have been developed and significant resources have been used to characterize hERG channel activities. However, evaluation of compound activities on hERG have not been performed for large compound collections due to technical difficulty, lack of throughput, and/or lack of biological relevance to function. Here we report a modified form of the FluxOR thallium flux assay, capable of measuring hERG activity in a homogeneous 1536-well plate format. To validate the assay, we screened a 7-point dilution series of the LOPAC 1280 library collection and reported rank order potencies of ten common hERG inhibitors. A correlation was also observed for the hERG channel activities of 10 known hERG inhibitors determined in this thallium flux assay and in the patch clamp experiment. Our findings indicate that this thallium flux assay can be used as an alternative method to profile large-volume compound libraries for compound activity on the hERG channel.
Proceedings of the National Academy of Sciences	Small-molecule agonists for the thyrotropin receptor stimulate thyroid function in human thyrocytes and mice. Neumann S, Huang W, Titus S, Krause G, Kleinau G, Alberobello AT, Zheng W, Southall NT, Inglese J, Austin CP, Celi FS, Gavrilova O, Thomas CJ, Raaka BM, Gershengorn MC. Seven-transmembrane-spanning receptors (7TMRs) are prominent drug targets. However, small-molecule ligands for 7-transmembrane-spanning receptors for which the natural ligands are large, heterodimeric glycoprotein hormones, like thyroid-stimulating hormone (TSH; thyrotropin), have only recently been reported, and none are approved for human use. We have used quantitative high-throughput screening to identify a small-molecule TSH receptor (TSHR) agonist that was modified to produce a second agonist with increased potency. We show that these agonists are highly selective for human TSHR versus other glycoprotein hormone receptors and interact with the receptor's serpentine domain. A binding pocket within the transmembrane domain was defined by docking into a TSHR homology model and was supported by site-directed mutagenesis. In primary cultures of human thyrocytes, both TSH and the agonists increase mRNA levels for thyroglobulin, thyroperoxidase, sodium iodide symporter, and deiodinase type 2, and deiodinase type 2 enzyme activity. Moreover, oral administration of the agonist stimulated thyroid function in mice, resulting in increased serum thyroxine and thyroidal radioiodide uptake. Thus, we discovered a small molecule that activates human TSHR in vitro, is orally active in mice, and could be a lead for development of drugs to use in place of recombinant human TSH in patients with thyroid cancer.
Journal of Biomolecular Screening	A New Homogeneous High Throughput Screening Assay for Profiling Compound Activity on the hERG Channel. Titus S, Beacham D, Shahane S, Southall N, Xia M, Huang R, Hooten E, Zhao Y, Shou L, Austin CP, Zheng W. Long QT syndrome, either inherited or acquired from drug treatments, can result in ventricular arrhythmia (Torsade de Pointes) and sudden death. hERG channel inhibition by drugs is now recognized as a common reason for the acquired form of Long QT syndrome. It has been reported that over 100 known drugs inhibit the activity of the hERG channel. Since 1997, several drugs have been withdrawn from the market due to the long QT syndrome caused by hERG inhibition. FDA regulations now require safety data on hERG channels for investigative new drug (IND) applications. The assessment of compound activity on the hERG channel has now become an important part of the safety evaluation in the process of drug discovery. In the last decade, several in vitro assay methods have been developed, and significant resources have been used to characterize hERG channel activities. However, evaluation of compound activities on hERG have not been performed for large compound collections due to technical difficulty, lack of throughput, or lack of biological relevance to function. We report here a modified form of the FluxOR(TM) thallium flux assay, capable of measuring hERG activity in a homogeneous 1536-well plate format. To validate the assay, we screened a 7 point dilution series of the LOPAC1280 collection and reported rank order potencies of eight common hERG inhibitors. A correlation was also observed for the hERG channel activities of 10 known hERG inhibitors determined in this thallium flux assay and in the patch clamp experiment. Our findings indicate that this thallium flux assay can be used as an alternative method to profile large volume compound libraries for compound activity on the hERG channel.
Analytical and Bioanalytical Chemistry	Synthesis and characterization of a new fluorogenic substrate for alpha-galactosidase. Shi ZD, Motabar O, Goldin E, Liu K, Southall N, Sidransky E, Austin CP, Griffiths GL, Zheng W. Alpha-galactosidase A hydrolyzes the terminal alpha-galactosyl moieties from glycolipids and glycoproteins in lysosomes. Mutations in alpha-galactosidase cause lysosomal accumulation of the glycosphingolipid, globotriaosylceramide, which leads to Fabry disease. Small-molecule chaperones that bind to mutant enzyme proteins and correct their misfolding and mistrafficking have emerged as a potential therapy for Fabry disease. We have synthesized a red fluorogenic substrate, resorufinyl alpha-D: -galactopyranoside, for a new alpha-galactosidase enzyme assay. This assay can be measured continuously at lower pH values, without the addition of a stop solution, due to the relatively low pK (a) of resorufin (~6). In addition, the assay emits red fluorescence, which can significantly reduce interferences due to compound fluorescence and dust/lint as compared to blue fluorescence. Therefore, this new red fluorogenic substrate and the resulting enzyme assay can be used in high-throughput screening to identify small-molecule chaperones for Fabry disease.
Bioorganic & Medicinal Chemistry	Quantitative high throughput screening identifies inhibitors of anthrax-induced cell death Zhu PJ, Hobson P, Southal NT, Qiu C, Thomas CJ, Lu J, Inglese J, Zheng W, Bugge TH, Austin CP Here, we report the results of a quantitative high-throughput screen (qHTS) measuring the endocytosis and translocation of a ß-lactamase-fused-lethal factor and the identification of small molecules capable of obstructing the process of anthrax toxin internalization. Several small molecules protect RAW264.7 macrophages and CHO cells from anthrax lethal toxin and protected cells from an LF-Pseudomonas exotoxin fusion protein and diphtheria toxin. Further efforts demonstrated that these compounds impaired the PA heptamer pre-pore to pore conversion in cells expressing the CMG2 receptor, but not the related TEM8 receptor, indicating that these compounds likely interfere with toxin internalization.
Journal of Biomolecular Screening	An Alphascreen-Based High-Throughput Screen to Identify Inhibitors of Hsp90-Cochaperone Interaction. Yi F, Zhu P, Southall N, Inglese J, Austin CP, Zheng W, Regan L. Hsp90 has emerged as an important anticancer drug target because of its essential role in promoting the folding and maturation of many oncogenic proteins. The authors describe the development of the first high-throughput screen, based on AlphaScreen(TM) technology, to identify a novel type of Hsp90 inhibitors that interrupt its interaction with the cochaperone HOP. The assay used 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 was stable over 12 h and tolerated DMSO up to 5%. The authors first validated the assay by screening against 20,000 compounds in a 384-well format. After further optimization into a 1536-well format, it was screened against an NIH Chemical Genomics Center library of 76,134 compounds, with a signal-to-background 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 anticancer drugs, for use alone or in combination with other Hsp90 inhibitors.
Proceedings of the National Academy of Sciences	Identification of compounds that potentiate CREB signaling as possible enhancers of long-term memory. Xia M, Huang R, Guo V, Southall N, Cho MH, Inglese J, Austin CP, Nirenberg M. Many studies have implicated the cAMP Response Element Binding (CREB) protein signaling pathway in long-term memory. To identify small molecule enhancers of CREB activation of gene expression, we screened approximately 73,000 compounds, each at 7-15 concentrations in a quantitative high-throughput screening (qHTS) format, for activity in cells by assaying CREB mediated beta-lactamase reporter gene expression. We identified 1,800 compounds that potentiated CREB mediated gene expression, with potencies as low as 16 nM, comprising 96 structural series. Mechanisms of action were systematically determined, and compounds that affect phosphodiesterase 4, protein kinase A, and cAMP production were identified, as well as compounds that affect CREB signaling via apparently unidentified mechanisms. qHTS folowed by interrogation of pathway targets is an efficient paradigm for lead generation for chemical genomics and drug development.
Journal of Medicinal Chemistry	A Basis for Reduced Chemical Library Inhibition of Firefly Luciferase Obtained from Directed Evolution Auld DS, Zhang YQ, Southall NT, Rai G, Landsman M, MacLure J, Langevin D, Thomas CJ, Austin CP, Inglese J We measured the “druggability” of the ATP-dependent luciferase derived from the firefly Photuris pennsylvanica that was optimized using directed evolution (Ultra-Glo, Promega). Quantitative high-throughput screening (qHTS) was used to determine IC50s of 198899 samples against a formulation of Ultra-Glo luciferase (Kinase-Glo). We found that only 0.1% of the Kinase-Glo inhibitors showed an IC50 < 10 µM compared to 0.9% found from a previous qHTS against the firefly luciferase from Photinus pyralis (lucPpy). Further, the maximum affinity identified in the lucPpy qHTS was 50 nM, while for Kinase-Glo this value increased to 600 nM. Compounds with interactions stretching outside the luciferin binding pocket were largely lost with Ultra-Glo luciferase. Therefore, Ultra-Glo luciferase will show less compound interference when used as an ATP sensor compared to lucPpy. This study demonstrates the power of large-scale quantitative analysis of structure-activity relationships (>100K compounds) in addressing important questions such as a target’s druggability.
PLoS Biology	COPI Complex Is a Regulator of Lipid Homeostasis Beller M, Sztalryd C, Southall N, Bell M, Jäckle H, Auld DS, Oliver B Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets.
Journal of Biomolecular Screening	A Cell-Based PDE4 Assay in 1536-Well Plate Format for High-Throughput Screening. Titus SA, Xiao L, Southall N, Lu J, Inglese J, Brasch M, Austin CP, Zheng W. The cyclic nucleotide phosphodiesterases (PDEs) are intracellular enzymes that catalyze the hydrolysis of 3,'5'-cyclic nucleotides, such as cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), to their corresponding 5'nucleotide monophosphates. These enzymes play an important role in controlling cellular concentrations of cyclic nucleotides and thus regulate a variety of cellular signaling events. PDEs are emerging as drug targets for several diseases, including asthma, cardiovascular disease, attention-deficit hyperactivity disorder, Parkinson's disease, and Alzheimer's disease. Although biochemical assays with purified recombinant PDE enzymes and cAMP or cGMP substrate are commonly used for compound screening, cell-based assays would provide a better assessment of compound activity in a more physiological context. The authors report the development and validation of a new cell-based PDE4 assay using a constitutively active G-protein-coupled receptor as a driving force for cAMP production and a cyclic nucleotide-gated cation channel as a biosensor in 1536-well plates.
Current Chemical Genomics	Comparison on Functional Assays for Gq-Coupled GPCRs by Measuring Inositol Monophospate-1 and Intracellular Calcium in 1536-Well Plate Format Liu K, Titus SA, Southall N, Zhu P, Inglese J, Austin CP, Zheng w. 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 (IP3) assay measures 3H-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 M1 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.
Bioorganic & Medicinal Chemistry Letters	Identification of a potent new chemotype for the selective inhibition of PDE4. Skoumbourdis AP, Huang R, Southall N, Leister W, Guo V, Cho MH, Inglese J, Nirenberg M, Austin CP, Xia M, Thomas CJ. A series of substituted 3,6-diphenyl-7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazines were prepared and analyzed as inhibitors of phosphodiesterase 4 (PDE4). Synthesis, structure–activity relationships, and the selectivity of a highly potent analogue against related phosphodiesterase isoforms are presented.
Chemical Research Toxicology	Characterization of Diversity in Toxicity Mechanism Using In Vitro Cytotoxicity Assays in Quantitative High Throughput Screening. Huang R, Southall N, Cho MH, Xia M, Inglese J, Austin CP. Assessing the potential health risks of environmental chemical compounds is an expensive undertaking which has motivated the development of new alternatives to traditional in vivo toxicological testing. One approach is to stage the evaluation, beginning with less expensive and higher throughput in vitro testing before progressing to more definitive trials. In vitro testing can be used to generate a hypothesis about a compound's mechanism of action, which can then be used to design an appropriate in vivo experiment. Here we begin to address the question of how to design such a battery of in vitro cell-based assays by combining data from two different types of assays, cell viability and caspase activation, with the aim of elucidating mechanism of action. Because caspase activation is a transient event during apoptosis, it is not possible to design a single end-point assay protocol that would identify all instances of compound-induced caspase activation. Nevertheless, useful information about compound mechanism of action can be obtained from these assays in combination with cell viability data. Unsupervised clustering in combination with Dunn's cluster validity index is a robust method for identifying mechanisms of action without requiring any a priori knowledge about mechanisms of toxicity. The performance of this clustering method is evaluated by comparing the clustering results against literature annotations of compound mechanisms.
Journal of Biomolecular Sciences	Quantitative High-Throughput Screening Using a Live-Cell cAMP Assay Identifies Small-Molecule Agonists of the TSH Receptor. Titus S, Neumann S, Zheng W, Southall N, Michael S, Klumpp C, Yasgar A, Shinn P, Thomas CJ, Inglese J, Gershengorn MC, Austin CP. The thyroid-stimulating hormone (TSH; thyrotropin) receptor belongs to the glycoprotein hormone receptor subfamily of 7transmembrane spanning receptors. TSH receptor (TSHR) is expressed mainly in thyroid follicular cells and is activated by TSH, which regulates the growth and function of thyroid follicular cells. Recombinant TSH is used in diagnostic screens for thyroid cancer, especially in patients after thyroid cancer surgery. Currently, no selective small-molecule agonists of the TSHR are available. To screen for novel TSHR agonists, the authors miniaturized a commercially available cell-based cyclic adenosine 3',5' monophosphate (cAMP) assay into a 1536-well plate format. This assay uses an HEK293 cell line stably transfected with the TSHR coupled to a cyclic nucleotide gated ion channel as a biosensor. From a quantitative high-throughput screen of 73,180 compounds in parallel with a parental cell line (without the TSHR), 276 primary active compounds were identified. The activities of the selected active compounds were further confirmed in an orthogonal homogeneous time-resolved fluorescence cAMP-based assay. Forty-nine compounds in several structural classes have been confirmed as the small-molecule TSHR agonists that will serve as a starting point for chemical optimization and studies of thyroid physiology in health and disease. PMID: 18216391
Journal of Medicinal Chemistry	Characterization of Chemical Libraries for Luciferase Inhibitory Activity. Auld DS, Southall N, Jadhav A, Johnson RL, Diller D, Simeonov S, Austin CP, Inglese J. To aid in the interpretation of HTS results derived from luciferase-based assays we used quantitative HTS (qHTS), an approach that defines the concentration-response behavior of each library sample, to profile the ATP-dependent luciferase from Photinus pyralis against >70,000 samples. We found approximately 3% of the library was active, containing only compounds with inhibitory concentration-responses of which 681 (0.9%) exhibited IC50s < 10 uM. Representative compounds were shown to inhibit purified P. pyralis as well as several commercial luciferase-based detection reagents but were found to be largely inactive against Renilla reniformis luciferase. Light attenuation by the samples was also examined and found to be more prominent in the blue-shifted bioluminescence produced by R. reniformas luciferase than with bioluminescence produced by P. pyralis luciferase. We describe the SAR of the luciferase inhibitors and discuss the use of this data in the interpretation of HTS results, and configuration of luciferase-based assays.
Journal of Medicinal Chemistry	Fluorescence Spectroscopic Profiling of Compound Libraries. Simeonov S, Jadhav A, Thomas CJ, Wang Y, Huang R, Southall N, Shinn P, Smith J, Austin CP, Inglese J. Chromo/fluorophoric properties often accompany the conjugated, aromatic and heterocyclic features of many of the scaffolds and impurities that make up library samples used for high throughput screening (HTS). These properties impart highly variable effects on assay outputs employing optical detection, thus complicating the interpretation of data and leading to false positives and negatives. Here, we report the comprehensive fluorescence profile of >70,000 samples across multiple spectral regions commonly utilized in HTS assays. The quantitative HTS (qHTS) paradigm was utilized to test each sample at seven or more concentration points over a 4-log concentration range in 1536-well format, with raw fluorescence response collected using a CCD-based imager. The resulting output was compared with fluorophore standards to compute a normalized fluorescence response (termed fluorophore-equivalent concentration, FEC) for each sample, concentration, and relevant spectral region. The greatest fraction of fluorescent compounds appeared in the UV-end of the light spectrum, where over 5% of library members matched or exceeded 10 nM FEC of 4-methylumbelliferone and AlexaFluor 350, while approximately 1.8% of the library matched or exceeded 100 nM FEC of these standards. Red-shifting the spectral window by as little as 100 nm was accompanied by a dramatic decrease in autofluorescence. Native compound fluorescence, scaffold overlap with known fluorophores, fluorescent impurities, novel fluorescent compounds, and the ability to discriminate generalities of fluorescent interferences and devise strategies to identify them are discussed.
Environmental Health Perspectives	Compound Cytotoxicity Profiling Using Quantitative High-Throughput Screening. Xia M, Huang R, Witt KL, Southall N, Fostel J, Cho MH, Jadhav A, Smith CS, Inglese J, Portier CJ, Tice RR, Austin CP. Background: The propensity of compounds to produce adverse health effects in humans is generally evaluated using animal-based test methods. Such methods can be relatively expensive, low-throughput, and associated with pain suffered by the treated animals. In addition, differences in species biology may confound extrapolation to human health effects. Objective: The U.S. National Toxicology Program and the NIH Chemical Genomics Center are collaborating to identify a battery of cell-based screens to prioritize compounds for further toxicological evaluation. Methods: 1,408 compounds previously tested in one or more traditional toxicological assays were profiled for cytotoxicity using quantitative high-throughput screening (qHTS) in 13 human and rodent cell types derived from six common targets of xenobiotic toxicity (liver, blood, kidney, nerve, lung, skin). Selected cytotoxicants were further tested to define response kinetics. Results: qHTS of these compounds produced robust and reproducible results which allowed cross-compound, cross-cell type, and cross-species comparisons. Some compounds were cytotoxic to all cell types at similar concentrations, while others exhibited species- or cell typespecific cytotoxicity. Closely related cell types and analogous cell types in human and rodent frequently showed different patterns of cytotoxicity. Some compounds inducing similar levels of cytotoxicity showed distinct time-dependence in kinetic studies, consistent with known mechanisms of toxicity. Conclusions: The generation of high-quality cytotoxicity data on this large library of known compounds using qHTS demonstrates the potential of this methodology to profile a much broader array of assays and compounds, which, in aggregate, may be valuable for prioritizing compounds for further toxicological evaluation, identifying compounds with particular mechanisms of action, and potentially predicting in vivo biological response
Bioorganic and Medicinal Chemistry Letters	Identification of N-(quinolin-8-yl)benzenesulfonamides as agents capable of down-regulating NFkappaB activity within two separate high-throughput screens of NFkappaB activation. Xie Y, Deng S, Thomas CJ, Liu Y, Zhang YQ, Rinderspacher A, Huang W, Gong G, Wyler M, Cayanis E, Aulner N, Többen U, Chung C, Pampou S, Southall N, Vidovic D, Schürer S, Branden L, Davis RE, Staudt LM, Inglese J, Austin CP, Landry DW, Smith DH, Auld DS. We describe here a series of N-(quinolin-8-yl)benzenesulfonamides capable of suppressing the NFkappaB pathway identified from two high-throughput screens run at two centers of the NIH Molecular Libraries Initiative. These small molecules were confirmed in both primary and secondary assays of NFkappaB activation and expanded upon through analogue synthesis. The series exhibited potencies in the cell-based assays at as low as 0.6muM, and several indications suggest that the targeted activity lies within a common region of the NFkappaB pathway.
ASSAY and Drug Development Technologies	A cell-based assay for IkappaBalpha stabilization using a two-color dual luciferase-based sensor. Davis RE, Zhang YQ, Southall N, Staudt LM, Austin CP, Inglese J, Auld DS. A cell-sensor assay for stabilization of IkappaBalpha was developed in the activated B cell-like diffuse large B-cell lymphoma cell line OCI-Ly3. This cell line expresses known nuclear factor kappaB (NFkappaB) target genes due to high constitutive activity of IkappaB kinase (IKK), which phosphorylates the protein IkappaBalpha leading to proteasomal degradation of IkappaBalpha and activation of NFkappaB. The cell-sensor assay uses green and red light-emitting beetle luciferases, with the green luciferase fused to IkappaBalpha (IkappaBalpha-CBG68) and the red luciferase (CBR) present in its native state. The IkappaBalpha-CBG68 reporter functions as a sensor of IKK and proteasome activity, while CBR serves to normalize for cell number and nonspecific effects. Both reporter constructs were stably integrated and placed under the control of an inducible promoter system, which increased fold responsiveness to inhibitors when assay incubations were performed simultaneous to reporter induction by doxycycline. The assay was miniaturized to a 1,536-well plate format and showed a Z' of 0.6; it was then used to panel 2,677 bioactive compounds by a concentration-response-based screening strategy. The concentration-effect curves for the IkappaBalpha-CBG68 and CBR signals were then used to identify specific stabilizers of IkappaBalpha, such as IKK inhibitors or proteasome inhibitors, which increased the doxycycline-induced rise in IkappaBalpha-CBG68 without affecting the rise in CBR. Known and unexpected inhibitors of NFkappaB signaling were identified from the bioactive collection. We describe here the development and performance of this assay, and discuss the merits of its specific features.
Journal of Medicinal Chemistry	Kinase patent space visualization using chemical replacements. Southall NT, Ajay Here we present a methodology for characterizing the structure of patented chemical space. This approach identifies those chemical replacements that can connect sets of exemplified compounds in individual patents. Chemists can then search these replacements to help them discover the architecture within their patent space of interest. To demonstrate the utility of such an approach, we characterize a set of kinase inhibitors from patents and literature and find that many companies' patents can be understood to be straightforward modifications of competitors' patents. By reapplying these same chemical themes to other related compound series, novel, biologically active compounds can be discovered.
Biophysical Chemistry	Potential of mean force between two hydrophobic solutes in water. Southall NT, Dill KA. We study the potential of mean force between two nonpolar solutes in the Mercedes Benz model of water. Using NPT Monte Carlo simulations, we find that the solute size determines the relative preference of two solute molecules to come into contact ('contact minimum') or to be separated by a single layer of water ('solvent-separated minimum'). Larger solutes more strongly prefer the contacting state, while smaller solutes have more tendency to become solvent-separated, particularly in cold water. The thermal driving forces oscillate with solute separation. Contacts are stabilized by entropy, whereas solvent-separated solute pairing is stabilized by enthalpy. The free energy of interaction for small solutes is well-approximated by scaled-particle theory. Copyright 2002 Elsevier Science B.V.
Journal of the American Chemical Society	How ions affect the structure of water. Hribar B, Southall NT, Vlachy V, Dill KA. We model ion solvation in water. We use the MB model of water, a simple two-dimensional statistical mechanical model in which waters are represented as Lennard-Jones disks having Gaussian hydrogen-bonding arms. We introduce a charge dipole into MB waters. We perform (NPT) Monte Carlo simulations to explore how water molecules are organized around ions and around nonpolar solutes in salt solutions. The model gives good qualitative agreement with experiments, including Jones-Dole viscosity B coefficients, Samoilov and Hirata ion hydration activation energies, ion solvation thermodynamics, and Setschenow coefficients for Hofmeister series ions, which describe the salt concentration dependence of the solubilities of hydrophobic solutes. The two main ideas captured here are (1) that charge densities govern the interactions of ions with water, and (2) that a balance of forces determines water structure: electrostatics (water's dipole interacting with ions) and hydrogen bonding (water interacting with neighboring waters). Small ions (kosmotropes) have high charge densities so they cause strong electrostatic ordering of nearby waters, breaking hydrogen bonds. In contrast, large ions (chaotropes) have low charge densities, and surrounding water molecules are largely hydrogen bonded.