@article {846706, title = {Chemical genetic modifier screens: small molecule trichostatin suppressors as probes of intracellular histone and tubulin acetylation.}, journal = {Chem Biol}, volume = {10}, year = {2003}, month = {2003 May}, pages = {397-410}, abstract = {

Histone deacetylase (HDAC) inhibitors are being developed as new clinical agents in cancer therapy, in part because they interrupt cell cycle progression in transformed cell lines. To examine cell cycle arrest induced by HDAC inhibitor trichostatin A (TSA), a cytoblot cell-based screen was used to identify small molecule suppressors of this process. TSA suppressors (ITSAs) counteract TSA-induced cell cycle arrest, histone acetylation, and transcriptional activation. Hydroxamic acid-based HDAC inhibitors like TSA and suberoylanilide hydroxamic acid (SAHA) promote acetylation of cytoplasmic alpha-tubulin as well as histones, a modification also suppressed by ITSAs. Although tubulin acetylation appears irrelevant to cell cycle progression and transcription, it may play a role in other cellular processes. Small molecule suppressors such as the ITSAs, available from chemical genetic suppressor screens, may prove to be valuable probes of many biological processes.

}, keywords = {Acetylation, Cell Cycle, Combinatorial Chemistry Techniques, Enzyme Inhibitors, Genetic techniques, Histone Deacetylase Inhibitors, Histones, Humans, Hydroxamic Acids, Molecular Structure, Promoter Regions, Genetic, Transcription, Genetic, Tubulin, Tumor Cells, Cultured}, issn = {1074-5521}, author = {Koeller, Kathryn M and Haggarty, Stephen J and Perkins, Brian D and Leykin, Igor and Wong, Jason C and Kao, Ming-Chih J and Schreiber, Stuart L.} } @article {846696, title = {A chemical genetic screen identifies inhibitors of regulated nuclear export of a Forkhead transcription factor in PTEN-deficient tumor cells.}, journal = {Cancer Cell}, volume = {4}, year = {2003}, month = {2003 Dec}, pages = {463-76}, abstract = {

The PI3K/PTEN/Akt signal transduction pathway plays a key role in many tumors. Downstream targets of this pathway include the Forkhead family of transcription factors (FOXO1a, FOXO3a, FOXO4). In PTEN null cells, FOXO1a is inactivated by PI3K-dependent phosphorylation and mislocalization to the cytoplasm, yet still undergoes nucleocytoplasmic shuttling. Since forcible localization of FOXO1a to the nucleus can reverse tumorigenicity of PTEN null cells, a high-content, chemical genetic screen for inhibitors of FOXO1a nuclear export was performed. The compounds detected in the primary screen were retested in secondary assays, and structure-function relationships were identified. Novel general export inhibitors were found that react with CRM1 as well as a number of compounds that inhibit PI3K/Akt signaling, among which are included multiple antagonists of calmodulin signaling.

}, keywords = {Active Transport, Cell Nucleus, Animals, Benzimidazoles, Benzothiazoles, Calmodulin, Cell Nucleus, DNA-Binding Proteins, Drug Design, Enzyme Inhibitors, Forkhead Transcription Factors, Gene Expression Regulation, Neoplastic, Humans, Karyopherins, Models, Molecular, Phosphatidylinositol 3-Kinases, Phosphoric Monoester Hydrolases, Phosphorylation, Receptors, Cytoplasmic and Nuclear, Signal Transduction, Transcription Factors, Tumor Cells, Cultured}, issn = {1535-6108}, author = {Kau, Tweeny R and Schroeder, Frank and Ramaswamy, Shivapriya and Wojciechowski, Cheryl L and Zhao, Jean J and Roberts, Thomas M and Clardy, Jon and Sellers, William R and Silver, Pamela A} } @article {846666, title = {Chemical genomic profiling of biological networks using graph theory and combinations of small molecule perturbations.}, journal = {J Am Chem Soc}, volume = {125}, year = {2003}, month = {2003 Sep 3}, pages = {10543-5}, abstract = {

Genome-wide measurements of multiple experimental samples yield rich fingerprints for comparison and interpretation. Here, a two-dimensional matrix of the cellular effects of all possible pairwise combinations of 24 small molecules, each with a different structure and bioactivity, was used to profile otherwise isogenic deletion strains of the yeast Saccharomyces cerevisiae. Using principles from graph theory, we derived a discrete model of the data for each strain by encoding the information in the form of a binary adjacency matrix. This matrix was used to construct a graph composed of nodes representing small molecules and edges connecting combinations that inhibited cell cycle progression. Computation of a set of graph theoretic descriptors for each chemical genetic network provided a topological fingerprint that showed genotype-dependent fluctuations. Because the structure of the genetic network determines the structure of the chemical genetic network, multidimensional chemical genomic profiling can be used for the characterization of perturbations in biological networks or the networks themselves. This application of small molecules could be useful for discerning the molecular basis of highly complex biological phenotypes, including those involved in the susceptibility to or etiology of human disease.

}, keywords = {Computer Graphics, Data Display, Data Interpretation, Statistical, Gene Deletion, Gene Expression Profiling, Saccharomyces cerevisiae}, issn = {0002-7863}, doi = {10.1021/ja035413p}, author = {Haggarty, Stephen J and Clemons, Paul A and Schreiber, Stuart L.} } @article {846656, title = {Determining the position of the cell division plane.}, journal = {Nature}, volume = {424}, year = {2003}, month = {2003 Aug 28}, pages = {1074-8}, abstract = {

Proper positioning of the cell division plane during mitosis is essential for determining the size and position of the two daughter cells--a critical step during development and cell differentiation. A bipolar microtubule array has been proposed to be a minimum requirement for furrow positioning in mammalian cells, with furrows forming at the site of microtubule plus-end overlap between the spindle poles. Observations in other species have suggested, however, that this may not be true. Here we show, by inducing mammalian tissue cells with monopolar spindles to enter anaphase, that furrow formation in cultured mammalian cells does not require a bipolar spindle. Unexpectedly, cytokinesis occurs at high frequency in monopolar cells. Division always occurs at a cortical position distal to the chromosomes. Analysis of microtubules during cytokinesis in cells with monopolar and bipolar spindles shows that a subpopulation of stable microtubules extends past chromosomes and binds to the cell cortex at the site of furrow formation. Our data are consistent with a model in which chromosomes supply microtubules with factors that promote microtubule stability and furrowing.

}, keywords = {Anaphase, Animals, Cell Differentiation, Cell Division, Cell Line, Cell Polarity, Chromosomes, microtubules, Mitosis, Pyrimidines, Spindle Apparatus, Thiones}, issn = {1476-4687}, doi = {10.1038/nature01860}, author = {Canman, Julie C and Cameron, Lisa A and Maddox, Paul S and Straight, Aaron and Tirnauer, Jennifer S and Mitchison, Timothy J and Fang, Guowei and Kapoor, Tarun M and Salmon, E D} } @article {846701, title = {Discovery of an inhibitor of a transcription factor using small molecule microarrays and diversity-oriented synthesis.}, journal = {J Am Chem Soc}, volume = {125}, year = {2003}, month = {2003 Jul 16}, pages = {8420-1}, abstract = {

Small molecule microarrays were screened to identify a small molecule ligand for Hap3p, a subunit of the yeast Hap2/3/4/5p transcription factor complex. The compound, named haptamide A, was determined to have a KD of 5.03 muM for binding to Hap3p using surface plasmon resonance analysis. Haptamide A also inhibited activation of a GDH1-lacZ reporter gene in a dose-dependent fashion. To explore structure-activity relationships, 11 derivatives of haptamide A were prepared using the same synthetic route that was developed for the original library synthesis. Analysis of dissociation constants and IC50 values for the reporter gene assay revealed a more potent inhibitor, haptamide B, with a KD of 330 nM. Whole-genome transcriptional profiling was used to compare effects of haptamide B with a hap3Delta yeast strain. Treatment with haptamide B, like the deletion mutant, reduced lactate-induced transcription of several genes from wild-type levels. Profiling the genetic "knockout" and the chemical genetic "knockdown" led to the identification of several genes that are regulated by Hap3p under nonfermentative conditions. These results demonstrate that a small molecule discovered using the small molecule microarray binding assay can permeate yeast cells and reach its target transcription factor protein in cells.

}, keywords = {Amides, CCAAT-Binding Factor, Combinatorial Chemistry Techniques, Fungal Proteins, Glutathione Transferase, Kinetics, Pyrans, Recombinant Fusion Proteins, Structure-Activity Relationship, Surface Plasmon Resonance, Transcription Factors}, issn = {0002-7863}, doi = {10.1021/ja0352698}, author = {Koehler, Angela N and Shamji, Alykhan F and Schreiber, Stuart L.} } @article {846711, title = {Dissecting temporal and spatial control of cytokinesis with a myosin II Inhibitor.}, journal = {Science}, volume = {299}, year = {2003}, month = {2003 Mar 14}, pages = {1743-7}, abstract = {

Completion of cell division during cytokinesis requires temporally and spatially regulated communication from the microtubule cytoskeleton to the actin cytoskeleton and the cell membrane. We identified a specific inhibitor of nonmuscle myosin II, blebbistatin, that inhibited contraction of the cleavage furrow without disrupting mitosis or contractile ring assembly. Using blebbistatin and other drugs, we showed that exit from the cytokinetic phase of the cell cycle depends on ubiquitin-mediated proteolysis. Continuous signals from microtubules are required to maintain the position of the cleavage furrow, and these signals control the localization of myosin II independently of other furrow components.

}, keywords = {Anaphase, Aurora Kinases, Cell Division, Cell Movement, Contractile Proteins, Cyclin-Dependent Kinases, DNA Replication, Enzyme Inhibitors, HeLa Cells, Heterocyclic Compounds with 4 or More Rings, Humans, Kinesin, Leupeptins, microtubules, Mitosis, Myosin Type II, Nocodazole, Protein-Serine-Threonine Kinases, Staurosporine, Ubiquitin}, issn = {1095-9203}, doi = {10.1126/science.1081412}, author = {Straight, Aaron F and Cheung, Amy and Limouze, John and Chen, Irene and Westwood, Nick J and Sellers, James R and Mitchison, Timothy J} } @article {846681, title = {Domain-selective small-molecule inhibitor of histone deacetylase 6 (HDAC6)-mediated tubulin deacetylation.}, journal = {Proc Natl Acad Sci U S A}, volume = {100}, year = {2003}, month = {2003 Apr 15}, pages = {4389-94}, abstract = {

Protein acetylation, especially histone acetylation, is the subject of both research and clinical investigation. At least four small-molecule histone deacetylase inhibitors are currently in clinical trials for the treatment of cancer. These and other inhibitors also affect microtubule acetylation. A multidimensional, chemical genetic screen of 7,392 small molecules was used to discover "tubacin," which inhibits alpha-tubulin deacetylation in mammalian cells. Tubacin does not affect the level of histone acetylation, gene-expression patterns, or cell-cycle progression. We provide evidence that class II histone deacetylase 6 (HDAC6) is the intracellular target of tubacin. Only one of the two catalytic domains of HDAC6 possesses tubulin deacetylase activity, and only this domain is bound by tubacin. Tubacin treatment did not affect the stability of microtubules but did decrease cell motility. HDAC6 overexpression disrupted the localization of p58, a protein that mediates binding of Golgi elements to microtubules. Our results highlight the role of alpha-tubulin acetylation in mediating the localization of microtubule-associated proteins. They also suggest that small molecules that selectively inhibit HDAC6-mediated alpha-tubulin deacetylation, a first example of which is tubacin, might have therapeutic applications as antimetastatic and antiangiogenic agents.

}, keywords = {3T3 Cells, Acetylation, Anilides, Animals, Cell Cycle, Cell Line, Dioxanes, Drug Evaluation, Preclinical, Enzyme Inhibitors, Gene Expression, Histone Deacetylase Inhibitors, Histone Deacetylases, Humans, Hydroxamic Acids, Jurkat Cells, Mice, Microtubule-Associated Proteins, microtubules, Protein Structure, Tertiary, Recombinant Proteins, Tubulin}, issn = {0027-8424}, doi = {10.1073/pnas.0430973100}, author = {Haggarty, Stephen J and Koeller, Kathryn M and Wong, Jason C and Grozinger, Christina M and Schreiber, Stuart L.} } @article {846661, title = {Exo1: a new chemical inhibitor of the exocytic pathway.}, journal = {Proc Natl Acad Sci U S A}, volume = {100}, year = {2003}, month = {2003 May 27}, pages = {6469-74}, abstract = {

A phenotypic screen was used to search for drug-like molecules that can interfere with specific steps in membrane traffic. 2-(4-Fluorobenzoylamino)-benzoic acid methyl ester (Exo1), identified in this screen, induces a rapid collapse of the Golgi to the endoplasmic reticulum, thus acutely inhibiting the traffic emanating from the endoplasmic reticulum. Like Brefeldin A (BFA), Exo1 induces the rapid release of ADP-ribosylation factor (ARF) 1 from Golgi membranes but has less effect on the organization of the trans-Golgi network. Our data indicate that Exo1 acts by a different mechanism from BFA. Unlike BFA, Exo1 does not induce the ADP-ribosylation of CtBP/Bars50 and does not interfere with the activity of guanine nucleotide exchange factors specific for Golgi-based ARFs. Thus, Exo1 allows the fatty acid exchange activity of Bars50 to be distinguished from ARF1 activity in the control of Golgi tubulation.

}, keywords = {Adenosine Diphosphate Ribose, Benzamides, Benzoates, Brefeldin A, Cell Line, Exocytosis, Golgi Apparatus, Guanine Nucleotide Exchange Factors, Microscopy, Fluorescence, Phenotype}, issn = {0027-8424}, doi = {10.1073/pnas.0631766100}, author = {Feng, Yan and Yu, Sidney and Lasell, Troy K R and Jadhav, Ashutosh P and Macia, Eric and Chardin, Pierre and Melancon, Paul and Roth, Michael and Mitchison, Timothy and Kirchhausen, Tomas} } @article {846646, title = {Expanding the functional group compatibility of small-molecule microarrays: discovery of novel calmodulin ligands.}, journal = {Angew Chem Int Ed Engl}, volume = {42}, year = {2003}, month = {2003 May 30}, pages = {2376-9}, keywords = {Calmodulin, Ligands}, issn = {1433-7851}, doi = {10.1002/anie.200351043}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&list_uids=12783500\&dopt=Abstract}, author = {Barnes-Seeman, David and Park, Seung Bum and Koehler, Angela N and Schreiber, Stuart L.} } @article {846686, title = {Identification of active-site inhibitors of MurG using a generalizable, high-throughput glycosyltransferase screen.}, journal = {J Am Chem Soc}, volume = {125}, year = {2003}, month = {2003 Sep 17}, pages = {11168-9}, abstract = {

MurG is a glycosyltransferase involved in the biosynthesis of bacterial peptidoglycan. It is a potentially important antibiotic target, but no inhibitors of the enzyme have been reported. In general, inhibitors of glycosyltransferases have been difficult to design. Furthermore, no glycosyltransferase inhibitors have been identified through high-throughput screening, perhaps because appropriate screens for glycosyltransferase inhibition have not been developed. In this manuscript, we describe the development of a high-throughput screen for MurG that was used to screen a 50 000 compound library for inhibitors. The screen, which can be generalized to other glycosyltransferases, led to the identification of a family of active-site directed MurG inhibitors. The family of inhibitors contains a five-membered heterocyclic core that appears to function as a diphosphate mimic with respect to the presentation of substituents. We discuss the implications of this result and the utility of the screen for identifying inhibitors of other glycosyltransferases.

}, keywords = {Anti-Bacterial Agents, Bacterial Outer Membrane Proteins, Binding Sites, Enzyme Inhibitors, Glycosyltransferases, Inhibitory Concentration 50, Molecular Structure, N-Acetylglucosaminyltransferases, Protein Conformation}, issn = {0002-7863}, doi = {10.1021/ja036494s}, author = {Helm, Jeremiah S and Hu, Yanan and Chen, Lan and Gross, Ben and Walker, Suzanne} } @article {846616, title = {Improved statistical methods for hit selection in high-throughput screening.}, journal = {J Biomol Screen}, volume = {8}, year = {2003}, month = {2003 Dec}, pages = {634-47}, keywords = {Algorithms, Drug Evaluation, Preclinical, Reference Standards, Statistics as Topic, Temperature}, issn = {1087-0571}, doi = {10.1177/1087057103258285}, author = {Brideau, Christine and Gunter, Bert and Pikounis, Bill and Liaw, Andy} } @article {846676, title = {Multidimensional chemical genetic analysis of diversity-oriented synthesis-derived deacetylase inhibitors using cell-based assays.}, journal = {Chem Biol}, volume = {10}, year = {2003}, month = {2003 May}, pages = {383-96}, abstract = {

Systematic chemical genetics aims to explore the space representing interactions between small molecules and biological systems. Beyond measuring binding interactions and enzyme inhibition, measuring changes in the activity of proteins in intact signaling networks is necessary. Toward this end, we are partitioning chemical space into regions with different biological activities using a panel of cell-based assays and small molecule "chemical genetic modifiers." Herein, we report on the use of this methodology for the discovery of 617 small molecule inhibitors of histone deacetylases from a multidimensional screen of an encoded, diversity-oriented synthesis library. Following decoding of chemical tags and resynthesis, we demonstrate the selectivity of one inhibitory molecule (tubacin) toward alpha-tubulin deacetylation and another (histacin) toward histone deacetylation. These small molecules will facilitate dissecting the role of acetylation in a variety of cell biological processes.

}, keywords = {Acetylation, Amidohydrolases, Anilides, Cell Line, Tumor, Combinatorial Chemistry Techniques, Enzyme Inhibitors, Genetic techniques, Histone Deacetylase Inhibitors, Humans, Hydroxamic Acids, Lysine, Molecular Structure, Principal Component Analysis, Structure-Activity Relationship, Tubulin}, issn = {1074-5521}, author = {Haggarty, Stephen J and Koeller, Kathryn M and Wong, Jason C and Butcher, Rebecca A and Schreiber, Stuart L.} } @article {846721, title = {Phenotypic screening of small molecule libraries by high throughput cell imaging.}, journal = {Comb Chem High Throughput Screen}, volume = {6}, year = {2003}, month = {2003 Jun}, pages = {279-86}, abstract = {

We have developed high throughput fluorescence cell imaging methods to screen chemical libraries for compounds with effects on diverse aspects of cell physiology. We describe screens for compounds that arrest cells in mitosis, that block cell migration, and that block the secretory pathway. Each of these screens yielded specific inhibitors for research use, and the mitosis screen identified Eg5 as a potential target protein for cancer chemotherapy. Cell imaging provides a large amount of information from primary screening data that can be used to distinguish compounds with different effects on cells, and together with automated analysis, to quantitate compound effects.

}, keywords = {Animals, Combinatorial Chemistry Techniques, Eukaryotic Cells, Humans, Image Processing, Computer-Assisted, Microscopy, Fluorescence, Phenotype}, issn = {1386-2073}, author = {Yarrow, J C and Feng, Y and Perlman, Z E and Kirchhausen, T and TJ Mitchison} } @article {846726, title = {SIR1, an upstream component in auxin signaling identified by chemical genetics.}, journal = {Science}, volume = {301}, year = {2003}, month = {2003 Aug 22}, pages = {1107-10}, abstract = {

Auxin is a plant hormone that regulates many aspects of plant growth and development. We used a chemical genetics approach to identify SIR1, a regulator of many auxin-inducible genes. The sir1 mutant was resistant to sirtinol, a small molecule that activates many auxin-inducible genes and promotes auxin-related developmental phenotypes. SIR1 is predicted to encode a protein composed of a ubiquitin-activating enzyme E1-like domain and a Rhodanese-like domain homologous to that of prolyl isomerase. We suggest a molecular context for how the auxin signal is propagated to exert its biological effects.

}, keywords = {Adenosine Triphosphate, Amino Acid Sequence, arabidopsis, Arabidopsis Proteins, Benzamides, Binding Sites, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Genes, Reporter, Indoleacetic Acids, Molecular Sequence Data, Mutation, Naphthols, Oligonucleotide Array Sequence Analysis, Phenotype, Plant Leaves, Plant Roots, Protein Structure, Tertiary, Signal Transduction, Sirtuins, Transcription, Genetic}, issn = {1095-9203}, doi = {10.1126/science.1084161}, author = {Zhao, Yunde and Dai, Xinhua and Blackwell, Helen E and Schreiber, Stuart L. and Chory, Joanne} } @article {846671, title = {Small molecule modulation of the human chromatid decatenation checkpoint.}, journal = {Chem Biol}, volume = {10}, year = {2003}, month = {2003 Dec}, pages = {1267-79}, abstract = {

After chromosome replication, the intertwined sister chromatids are disentangled by topoisomerases. The integrity of this process is monitored by the chromatid decatenation checkpoint. Here, we describe small molecule modulators of the human chromatid decatenation checkpoint identified using a cell-based, chemical genetic modifier screen. Similar to 1,2,7-trimethylyxanthine (caffeine), these small molecules suppress the G(2)-phase arrest caused by ICRF-193, a small molecule inhibitor of the enzymatic activity of topoisomerase II. Analysis of specific suppressors, here named suptopins for suppressor of Topoisomerase II inhibition, revealed distinct effects on cell cycle progression, microtubule stability, nucleocytoplasmic transport of cyclin B1, and no effect on the chromatin deacetylation checkpoint induced by trichostatin A. The suptopins provide new molecular tools for dissecting the role of topoisomerases in maintaining genomic stability and determining whether inhibiting the chromatid decatenation checkpoint sensitizes tumor cells to chemotherapeutics.

}, keywords = {Acetylation, Aminophenols, Benzazepines, Cell Cycle, Cell Line, Tumor, Cell Nucleus, Chromatids, Cyclin B, Cyclin B1, DNA Topoisomerases, Type II, Fluorescent Antibody Technique, Genes, cdc, Humans, Hydroxamic Acids, microtubules, Mitosis, Molecular Structure, Piperazines, Protein Transport, Pyrones, Spindle Apparatus, Thiazoles, Topoisomerase II Inhibitors}, issn = {1074-5521}, author = {Haggarty, Stephen J and Koeller, Kathryn M and Kau, Tweeny R and Silver, Pamela A and Roberge, Michel and Schreiber, Stuart L.} } @article {846651, title = {A small molecule suppressor of FK506 that targets the mitochondria and modulates ionic balance in Saccharomyces cerevisiae.}, journal = {Chem Biol}, volume = {10}, year = {2003}, month = {2003 Jun}, pages = {521-31}, abstract = {

FK506 inhibits the evolutionarily conserved, Ca(2+)-dependent phosphatase calcineurin, which in yeast is essential for growth during sodium stress. We undertook a chemical genetic modifier screen to identify small molecules that suppress the ability of FK506 to inhibit yeast growth in high NaCl. One of these small molecule suppressors, SFK1 (suppressor of FK506 1), causes a mitochondrially induced death in low salt, concomitant with the release of reactive oxygen species. Biochemically, SFK1 interacts with Por1p, a channel protein in the outer mitochondrial membrane, suggesting that SFK1 interacts with the mitochondria directly. A genome-wide screen of yeast deletion strains for hypersensitivity to SFK1 yielded several strains with impaired mitochondrial function, as well as several with reduced sodium tolerance. Our data link ionic balance to mitochondrial function and suggest a role for calcineurin in mediating this signaling network.

}, keywords = {Apoptosis, Calcineurin, Cyclohexanes, DNA-Binding Proteins, Intracellular Membranes, Intracellular Signaling Peptides and Proteins, ion channels, mitochondria, Molecular Structure, Oxidative Phosphorylation, Porins, Protein Kinases, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Signal Transduction, Sodium Chloride, Structure-Activity Relationship, Tacrolimus}, issn = {1074-5521}, author = {Butcher, Rebecca A and Schreiber, Stuart L.} } @article {846716, title = {Structural biasing elements for in-cell histone deacetylase paralog selectivity.}, journal = {J Am Chem Soc}, volume = {125}, year = {2003}, month = {2003 May 14}, pages = {5586-7}, abstract = {

We use the structural dissection of two 1,3-dioxanes with in-cell histone deacetylase (HDAC) paralog selectivity to identify key elements for selective HDAC inhibitors. We demonstrate that o-aminoanilides are inactive toward HDAC6 while apparently inhibiting deacetylases that act upon histone substrates. This finding has important clinical implications for the development of HDAC inhibitor-based treatments that do not interfere with microtubule dynamics associated with HDAC6. We also show that suberoylanilide hydroxamic acid (SAHA) alone is a nonparalog-selective HDAC inhibitor and that the 1,3-dioxane diversity appended to SAHA is essential for HDAC6 paralog selectivity.

}, keywords = {Anilides, Dioxanes, Enzyme Inhibitors, Histone Deacetylase Inhibitors, Histone Deacetylases, Humans, Hydroxamic Acids, Structure-Activity Relationship}, issn = {0002-7863}, doi = {10.1021/ja0341440}, author = {Wong, Jason C and Hong, Roger and Schreiber, Stuart L.} } @article {846691, title = {Virtual screening to enrich hit lists from high-throughput screening: a case study on small-molecule inhibitors of angiogenin.}, journal = {Proteins}, volume = {50}, year = {2003}, month = {2003 Jan 1}, pages = {81-93}, abstract = {

"Hit lists" generated by high-throughput screening (HTS) typically contain a large percentage of false positives, making follow-up assays necessary to distinguish active from inactive substances. Here we present a method for improving the accuracy of HTS hit lists by computationally based virtual screening (VS) of the corresponding chemical libraries and selecting hits by HTS/VS consensus. This approach was applied in a case study on the target-enzyme angiogenin, a potent inducer of angiogenesis. In conjunction with HTS of the National Cancer Institute Diversity Set and ChemBridge DIVERSet E (approximately 18,000 compounds total), VS was performed with two flexible library docking/scoring methods, DockVision/Ludi and GOLD. Analysis of the results reveals that dramatic enrichment of the HTS hit rate can be achieved by selecting compounds in consensus with one or both of the VS functions. For example, HTS hits ranked in the top 2\% by GOLD included 42\% of the true hits, but only 8\% of the false positives; this represents a sixfold enrichment over the HTS hit rate. Notably, the HTS/VS method was effective in selecting out inhibitors with midmicromolar dissociation constants typical of leads commonly obtained in primary screens.

}, keywords = {Binding Sites, Computational Biology, Computer Simulation, Databases, Factual, Enzyme Inhibitors, Ligands, Models, Molecular, Reproducibility of Results, Ribonuclease, Pancreatic}, issn = {1097-0134}, doi = {10.1002/prot.10270}, author = {Jenkins, Jeremy L and Kao, Richard Y T and Shapiro, Robert} } @article {844031, title = {A Simple Technique for Reducing Edge Effect in Cell-Based Assays.}, journal = {J Biomol Screen }, volume = {8}, year = {2003}, month = {Oct}, pages = {566-570}, author = {BK Lundholt and KM Scudder and L Pagliaro} } @article {841066, title = {Development and Application of Fluorescence Polarization Assays in Drug Discovery.}, journal = {Comb Chem High Throughput Screen }, volume = {6}, year = {2003}, month = {May}, pages = {183-94}, author = {TJ Burke and KR Loniello and JA Beebe and KM Ervin} } @article {841036, title = {Fluorescence Polarization: Past, Present and Future.}, journal = {Comb Chem High Throughput Screen}, volume = {6}, year = {2003}, month = {May}, pages = {167-73}, author = {DM Jameson and JC Croney} }