151
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Dranchak P, Moran JJ, MacArthur R, Lopez-Anido C, Inglese J, Svaren J. Genome-Edited Cell Lines for High-Throughput Screening. Methods Mol Biol 2018; 1755:1-17. [PMID: 29671259 DOI: 10.1007/978-1-4939-7724-6_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Measurement of gene expression for high-throughput screening is an increasingly used technique that has been developed for not only gene dosage disorders resulting from disease-associated copy number variations, but also for induction/repression of genes modulating the severity of a disease phenotype. Traditional methods have employed transient or stable transfection of reporter constructs in which a single reporter is driven by selected regulatory elements from the candidate gene. However, individual regulatory elements are inherently unable to capture the integrated regulation of multiple enhancers at the endogenous locus, and random reporter insertion can result in neighborhood effects that impact the physiological responsiveness of the reporter. Therefore, we outline a general method of employing genome editing to insert reporters into the 3' UTR of a candidate gene, which has been used successfully in our studies of the Pmp22 gene associated with Charcot-Marie-Tooth disease. The method employs genome editing to insert two nonhomologous reporters that maximize the efficiency of identification of biologically active molecules through concordant responses in small molecule screening. We include a number of aspects of the design and construction of these reporter assays that will be applicable to creation of similar assays in a variety of cell types.
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Affiliation(s)
- Patricia Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - John J Moran
- Waisman Center, University of Wisconsin, Madison, WI, USA
| | - Ryan MacArthur
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | | | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - John Svaren
- Waisman Center, University of Wisconsin, Madison, WI, USA. .,Department of Comparative Biosciences, University of Wisconsin, Madison, WI, USA.
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152
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153
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154
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He M, Han Z, Liu L, Zheng YG. Untersuchung der epigenetischen Funktionen von Lysin‐Acetyltransferasen mit Methoden der chemischen Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Maomao He
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Zhen Han
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Liang Liu
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Y. George Zheng
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
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155
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He M, Han Z, Liu L, Zheng YG. Chemical Biology Approaches for Investigating the Functions of Lysine Acetyltransferases. Angew Chem Int Ed Engl 2017; 57:1162-1184. [PMID: 28786225 DOI: 10.1002/anie.201704745] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 12/20/2022]
Abstract
The side-chain acetylation of lysine residues in histones and non-histone proteins catalyzed by lysine acetyltransferases (KATs) represents a widespread posttranslational modification (PTM) in the eukaryotic cells. Lysine acetylation plays regulatory roles in major cellular pathways inside and outside the nucleus. In particular, KAT-mediated histone acetylation has an effect on all DNA-templated epigenetic processes. Aberrant expression and activation of KATs are commonly observed in human diseases, especially cancer. In recent years, the study of KAT functions in biology and disease has greatly benefited from chemical biology tools and strategies. In this Review, we present the past and current accomplishments in the design of chemical biology approaches for the interrogation of KAT activity and function. These methods and probes are classified according to their mechanisms of action and respective applications, with both strengths and limitations discussed.
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Affiliation(s)
- Maomao He
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Zhen Han
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Liang Liu
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Y George Zheng
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
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156
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A Luciferase Reporter Gene System for High-Throughput Screening of γ-Globin Gene Activators. Methods Mol Biol 2017; 1439:207-26. [PMID: 27316998 DOI: 10.1007/978-1-4939-3673-1_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Luciferase reporter gene assays have long been used for drug discovery due to their high sensitivity and robust signal. A dual reporter gene system contains a gene of interest and a control gene to monitor non-specific effects on gene expression. In our dual luciferase reporter gene system, a synthetic promoter of γ-globin gene was constructed immediately upstream of the firefly luciferase gene, followed downstream by a synthetic β-globin gene promoter in front of the Renilla luciferase gene. A stable cell line with the dual reporter gene was cloned and used for all assay development and HTS work. Due to the low activity of the control Renilla luciferase, only the firefly luciferase activity was further optimized for HTS. Several critical factors, such as cell density, serum concentration, and miniaturization, were optimized using tool compounds to achieve maximum robustness and sensitivity. Using the optimized reporter assay, the HTS campaign was successfully completed and approximately 1000 hits were identified. In this chapter, we also describe strategies to triage hits that non-specifically interfere with firefly luciferase.
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157
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Holdgate GA, Meek TD, Grimley RL. Mechanistic enzymology in drug discovery: a fresh perspective. Nat Rev Drug Discov 2017; 17:115-132. [PMID: 29192286 DOI: 10.1038/nrd.2017.219] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Given the therapeutic and commercial success of small-molecule enzyme inhibitors, as exemplified by kinase inhibitors in oncology, a major focus of current drug-discovery and development efforts is on enzyme targets. Understanding the course of an enzyme-catalysed reaction can help to conceptualize different types of inhibitor and to inform the design of screens to identify desired mechanisms. Exploiting this information allows the thorough evaluation of diverse compounds, providing the knowledge required to efficiently optimize leads towards differentiated candidate drugs. This review highlights the rationale for conducting high-quality mechanistic enzymology studies and considers the added value in combining such studies with orthogonal biophysical methods.
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Affiliation(s)
- Geoffrey A Holdgate
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| | - Thomas D Meek
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Rachel L Grimley
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
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158
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Assay interference and off-target liabilities of reported histone acetyltransferase inhibitors. Nat Commun 2017; 8:1527. [PMID: 29142305 PMCID: PMC5688144 DOI: 10.1038/s41467-017-01657-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 10/06/2017] [Indexed: 12/20/2022] Open
Abstract
Many compounds with potentially reactive chemical motifs and poor physicochemical properties are published as selective modulators of biomolecules without sufficient validation and then propagated in the scientific literature as useful chemical probes. Several histone acetyltransferase (HAT) inhibitors with these liabilities are now routinely used to probe epigenetic pathways. We profile the most commonly used HAT inhibitors and confirm that the majority of them are nonselective interference compounds. Most (15 out of 23, 65%) of the inhibitors are flagged by ALARM NMR, an industry-developed counter-screen for promiscuous compounds. Biochemical counter-screens confirm that most of these compounds are either thiol-reactive or aggregators. Selectivity panels show many of these compounds modulate unrelated targets in vitro, while several also demonstrate nonspecific effects in cell assays. These data demonstrate the usefulness of performing counter-screens for bioassay promiscuity and assay interference, and raise caution about the utility of many widely used, but insufficiently validated, compounds employed in chemical biology. A substantial obstacle in basic research is the use of poorly validated tool compounds with purported useful biological functions. Here, the authors systematically profile widely used histone acetyltransferase inhibitors and find that the majority are nonselective interference compounds.
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159
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Morreale FE, Testa A, Chaugule VK, Bortoluzzi A, Ciulli A, Walden H. Mind the Metal: A Fragment Library-Derived Zinc Impurity Binds the E2 Ubiquitin-Conjugating Enzyme Ube2T and Induces Structural Rearrangements. J Med Chem 2017; 60:8183-8191. [PMID: 28933844 PMCID: PMC5663392 DOI: 10.1021/acs.jmedchem.7b01071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Efforts
to develop inhibitors, activators, and effectors of biological
reactions using small molecule libraries are often hampered by interference
compounds, artifacts, and false positives that permeate the pool of
initial hits. Here, we report the discovery of a promising initial
hit compound targeting the Fanconi anemia ubiquitin-conjugating enzyme
Ube2T and describe its biophysical and biochemical characterization.
Analysis of the co-crystal structure led to the identification of
a contaminating zinc ion as solely responsible for the observed effects.
Zinc binding to the active site cysteine induces a domain swap in
Ube2T that leads to cyclic trimerization organized in an open-ended
linear assembly. Our study serves as a cautionary tale for screening
small molecule libraries and provides insights into the structural
plasticity of ubiquitin-conjugating enzymes.
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Affiliation(s)
- Francesca E Morreale
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
| | - Andrea Testa
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
| | - Viduth K Chaugule
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
| | - Alessio Bortoluzzi
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
| | - Alessio Ciulli
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
| | - Helen Walden
- MRC Protein Phosphorylation and Ubiquitylation Unit, ‡Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom
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160
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Salas-Sarduy E, Landaburu LU, Karpiak J, Madauss KP, Cazzulo JJ, Agüero F, Alvarez VE. Novel scaffolds for inhibition of Cruzipain identified from high-throughput screening of anti-kinetoplastid chemical boxes. Sci Rep 2017; 7:12073. [PMID: 28935948 PMCID: PMC5608908 DOI: 10.1038/s41598-017-12170-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/04/2017] [Indexed: 11/16/2022] Open
Abstract
American Trypanosomiasis or Chagas disease is a prevalent, neglected and serious debilitating illness caused by the kinetoplastid protozoan parasite Trypanosoma cruzi. The current chemotherapy is limited only to nifurtimox and benznidazole, two drugs that have poor efficacy in the chronic phase and are rather toxic. In this scenario, more efficacious and safer drugs, preferentially acting through a different mechanism of action and directed against novel targets, are particularly welcome. Cruzipain, the main papain-like cysteine peptidase of T. cruzi, is an important virulence factor and a chemotherapeutic target with excellent pre-clinical validation evidence. Here, we present the identification of new Cruzipain inhibitory scaffolds within the GlaxoSmithKline HAT (Human African Trypanosomiasis) and Chagas chemical boxes, two collections grouping 404 non-cytotoxic compounds with high antiparasitic potency, drug-likeness, structural diversity and scientific novelty. We have adapted a continuous enzymatic assay to a medium-throughput format and carried out a primary screening of both collections, followed by construction and analysis of dose-response curves of the most promising hits. Using the identified compounds as a starting point a substructure directed search against CHEMBL Database revealed plausible common scaffolds while docking experiments predicted binding poses and specific interactions between Cruzipain and the novel inhibitors.
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Affiliation(s)
- Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad Nacional de San Martín - CONICET, San Martin, B1650HMP, Buenos Aires, Argentina
| | - Lionel Urán Landaburu
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad Nacional de San Martín - CONICET, San Martin, B1650HMP, Buenos Aires, Argentina
| | - Joel Karpiak
- GlaxoSmithKline R&D, Molecular Design US, Pennsylvania, Upper Providence PA, USA
| | - Kevin P Madauss
- GlaxoSmithKline R&D, Trust in Science, Pennsylvania, Upper Providence PA, USA
| | - Juan José Cazzulo
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad Nacional de San Martín - CONICET, San Martin, B1650HMP, Buenos Aires, Argentina
| | - Fernán Agüero
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad Nacional de San Martín - CONICET, San Martin, B1650HMP, Buenos Aires, Argentina.
| | - Vanina Eder Alvarez
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad Nacional de San Martín - CONICET, San Martin, B1650HMP, Buenos Aires, Argentina.
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161
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Martin Del Campo JS, Eckshtain-Levi M, Vogelaar NJ, Sobrado P. Identification of Aspergillus fumigatus UDP-Galactopyranose Mutase Inhibitors. Sci Rep 2017; 7:10836. [PMID: 28883473 PMCID: PMC5589893 DOI: 10.1038/s41598-017-11022-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/17/2017] [Indexed: 01/08/2023] Open
Abstract
Aspergillus fumigatus is an opportunistic human pathogen responsible for deadly, invasive infections in immunocompromised patients. The A. fumigatus cell wall is a complex network of polysaccharides among them galactofuran, which is absent in humans. UDP-galactopyranose mutase (UGM) catalyzes the conversion of UDP-galactofuranose (UDP-Galf) to UDP-galactopyranose (UDP-Galp) and is an important virulence factor. UGM is a flavin-dependent enzyme that requires the reduced flavin for activity; flavin reduction is achieved by reaction with NADPH. The aim of this work was to discover inhibitors of UGM by targeting the NADPH binding site using an ADP-TAMRA probe in a high-throughput screening assay. The flavonoids (2S)-hesperetin and (2S)-naringenin were validated as competitive inhibitors of UGM against NADPH with Ki values of 6 µM and 74 µM, respectively. To gain insight into the active chemical substituents involved in the inhibition of UGM, several derivatives of these inhibitors were studied. The results show that the hydroxyl groups of (2S)-hesperetin are important for inhibition, in particular the phenyl-chroman moiety. Congo red susceptibility assay and growth temperature effects showed that these compounds affected cell wall biosynthesis in A. fumigatus. This work is the first report of inhibition studies on UGM from eukaryotic human pathogens.
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Affiliation(s)
| | | | - Nancy J Vogelaar
- Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA. .,Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA.
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162
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Beeman K, Baumgärtner J, Laubenheimer M, Hergesell K, Hoffmann M, Pehl U, Fischer F, Pieck JC. Integration of an In Situ MALDI-Based High-Throughput Screening Process: A Case Study with Receptor Tyrosine Kinase c-MET. SLAS DISCOVERY 2017; 22:1203-1210. [DOI: 10.1177/2472555217727701] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Mass spectrometry (MS) is known for its label-free detection of substrates and products from a variety of enzyme reactions. Recent hardware improvements have increased interest in the use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS for high-throughput drug discovery. Despite interest in this technology, several challenges remain and must be overcome before MALDI-MS can be integrated as an automated “in-line reader” for high-throughput drug discovery. Two such hurdles include in situ sample processing and deposition, as well as integration of MALDI-MS for enzymatic screening assays that usually contain high levels of MS-incompatible components. Here we adapt our c-MET kinase assay to optimize for MALDI-MS compatibility and test its feasibility for compound screening. The pros and cons of the Echo (Labcyte) as a transfer system for in situ MALDI-MS sample preparation are discussed. We demonstrate that this method generates robust data in a 1536-grid format. We use the MALDI-MS to directly measure the ratio of c-MET substrate and phosphorylated product to acquire IC50 curves and demonstrate that the pharmacology is unaffected. The resulting IC50 values correlate well between the common label-based capillary electrophoresis and the label-free MALDI-MS detection method. We predict that label-free MALDI-MS-based high-throughput screening will become increasingly important and more widely used for drug discovery.
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Affiliation(s)
- Katrin Beeman
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Jens Baumgärtner
- Analytics Healthcare, Biomolecule Analytics, Merck KGaA, Darmstadt, Germany
| | - Manuel Laubenheimer
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Karlheinz Hergesell
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Martin Hoffmann
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Ulrich Pehl
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Frank Fischer
- Analytics Healthcare, Biomolecule Analytics, Merck KGaA, Darmstadt, Germany
| | - Jan-Carsten Pieck
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
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163
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Sanders JM, Beshore DC, Culberson JC, Fells JI, Imbriglio JE, Gunaydin H, Haidle AM, Labroli M, Mattioni BE, Sciammetta N, Shipe WD, Sheridan RP, Suen LM, Verras A, Walji A, Joshi EM, Bueters T. Informing the Selection of Screening Hit Series with in Silico Absorption, Distribution, Metabolism, Excretion, and Toxicity Profiles. J Med Chem 2017; 60:6771-6780. [DOI: 10.1021/acs.jmedchem.6b01577] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- John M. Sanders
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Douglas C. Beshore
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - J. Christopher Culberson
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - James I. Fells
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Jason E. Imbriglio
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Hakan Gunaydin
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Andrew M. Haidle
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Marc Labroli
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Brian E. Mattioni
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Nunzio Sciammetta
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - William D. Shipe
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Robert P. Sheridan
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Linda M. Suen
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Andreas Verras
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Abbas Walji
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Elizabeth M. Joshi
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Tjerk Bueters
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
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164
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Ibáñez G, Calder PA, Radu C, Bhinder B, Shum D, Antczak C, Djaballah H. Evaluation of Compound Optical Interference in High-Content Screening. SLAS DISCOVERY 2017; 23:321-329. [PMID: 28467117 DOI: 10.1177/2472555217707725] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Compound optical interference remains an inherent problem in chemical screening and has been well documented for biochemical assays and less so for automated microscopy-based assays. It has also been the assumption that the latter should not suffer from such interference because of the washing steps involved in the process, thus eliminating the residual nonspecific compound effects. Instead, these compounds may have no relevance to the actual target, and as such, compound optical interference contributes to a number of false-positives, resulting in a high attrition rate during subsequent follow-up studies. In this report, we analyze the outcome of a high-content screen using enhanced green fluorescent protein as a reporter in a gain-of-function cell-based assay in search of modulators of the micro RNA (miRNA) biogenesis pathway. Using a previously validated image-based biosensor, we screened a diverse library collection of ~315,000 compounds covering natural and synthetic derivatives in which 1130 positives were identified to enhance green fluorescence expression. Lateral confirmation and dose-response studies revealed that all of these compounds were the result of optical interference and not specific inhibition of miRNA biogenesis. Here, we highlight the chemical classes that are susceptible to compound optical interference and discuss their implications in automated microscopy-based assays.
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Affiliation(s)
- Glorymar Ibáñez
- 1 Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.,2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul A Calder
- 1 Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.,2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Constantin Radu
- 3 Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Bhavneet Bhinder
- 2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,4 Weill Cornell Medicine, New York, NY, USA
| | - David Shum
- 2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,3 Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Christophe Antczak
- 2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,5 Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Hakim Djaballah
- 2 HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,6 Keren Therapeutics, Scarsdale, NY, USA
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165
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Gul S. Epigenetic assays for chemical biology and drug discovery. Clin Epigenetics 2017; 9:41. [PMID: 28439316 PMCID: PMC5399855 DOI: 10.1186/s13148-017-0342-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 04/12/2017] [Indexed: 12/27/2022] Open
Abstract
The implication of epigenetic abnormalities in many diseases and the approval of a number of compounds that modulate specific epigenetic targets in a therapeutically relevant manner in cancer specifically confirms that some of these targets are druggable by small molecules. Furthermore, a number of compounds are currently in clinical trials for other diseases including cardiovascular, neurological and metabolic disorders. Despite these advances, the approved treatments for cancer only extend progression-free survival for a relatively short time and being associated with significant side effects. The current clinical trials involving the next generation of epigenetic drugs may address the disadvantages of the currently approved epigenetic drugs. The identification of chemical starting points of many drugs often makes use of screening in vitro assays against libraries of synthetic or natural products. These assays can be biochemical (using purified protein) or cell-based (using for example, genetically modified, cancer cell lines or primary cells) and performed in microtiter plates, thus enabling a large number of samples to be tested. A considerable number of such assays are available to monitor epigenetic target activity, and this review provides an overview of drug discovery and chemical biology and describes assays that monitor activities of histone deacetylase, lysine-specific demethylase, histone methyltransferase, histone acetyltransferase and bromodomain. It is of critical importance that an appropriate assay is developed and comprehensively validated for a given drug target prior to screening in order to improve the probability of the compound progressing in the drug discovery value chain.
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Affiliation(s)
- Sheraz Gul
- Fraunhofer Institute for Molecular Biology and Applied Ecology - ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
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166
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Infect Dis 2017; 3:259-262. [PMID: 28244723 DOI: 10.1021/acsinfecdis.7b00023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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167
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Med Chem Lett 2017; 8:379-382. [PMID: 28435522 DOI: 10.1021/acsmedchemlett.7b00056] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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168
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Schuck BW, MacArthur R, Inglese J. Quantitative High-Throughput Screening Using a Coincidence Reporter Biocircuit. CURRENT PROTOCOLS IN NEUROSCIENCE 2017; 79:5.32.1-5.32.27. [PMID: 28398644 PMCID: PMC5510169 DOI: 10.1002/cpns.27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Reporter-biased artifacts-i.e., compounds that interact directly with the reporter enzyme used in a high-throughput screening (HTS) assay and not the biological process or pharmacology being interrogated-are now widely recognized to reduce the efficiency and quality of HTS used for chemical probe and therapeutic development. Furthermore, narrow or single-concentration HTS perpetuates false negatives during primary screening campaigns. Titration-based HTS, or quantitative HTS (qHTS), and coincidence reporter technology can be employed to reduce false negatives and false positives, respectively, thereby increasing the quality and efficiency of primary screening efforts, where the number of compounds investigated can range from tens of thousands to millions. The three protocols described here allow for generation of a coincidence reporter (CR) biocircuit to interrogate a biological or pharmacological question of interest, generation of a stable cell line expressing the CR biocircuit, and qHTS using the CR biocircuit to efficiently identify high-quality biologically active small molecules. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Brittany W Schuck
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Ryan MacArthur
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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169
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Li S, Huang R, Solomon S, Liu Y, Zhao B, Santillo MF, Xia M. Identification of acetylcholinesterase inhibitors using homogenous cell-based assays in quantitative high-throughput screening platforms. Biotechnol J 2017; 12. [PMID: 28294544 DOI: 10.1002/biot.201600715] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/09/2017] [Accepted: 03/13/2017] [Indexed: 12/31/2022]
Abstract
Acetylcholinesterase (AChE) is an enzyme responsible for metabolism of acetylcholine, a neurotransmitter associated with muscle movement, cognition, and other neurobiological processes. Inhibition of AChE activity can serve as a therapeutic mechanism, but also cause adverse health effects and neurotoxicity. In order to efficiently identify AChE inhibitors from large compound libraries, homogenous cell-based assays in high-throughput screening platforms are needed. In this study, a fluorescent method using Amplex Red (10-acetyl-3,7-dihydroxyphenoxazine) and the Ellman absorbance method were both developed in a homogenous format using a human neuroblastoma cell line (SH-SY5Y). An enzyme-based assay using Amplex Red was also optimized and used to confirm the potential inhibitors. These three assays were used to screen 1368 compounds, which included a library of pharmacologically active compounds (LOPAC) and 88 additional compounds from the Tox21 program, at multiple concentrations in a quantitative high-throughput screening (qHTS) format. All three assays exhibited exceptional performance characteristics including assay signal quality, precision, and reproducibility. A group of inhibitors were identified from this study, including known (e.g. physostigmine and neostigmine bromide) and potential novel AChE inhibitors (e.g. chelerythrine chloride and cilostazol). These results demonstrate that this platform is a promising means to profile large numbers of chemicals that inhibit AChE activity.
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Affiliation(s)
- Shuaizhang Li
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA.,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ruili Huang
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Solomon
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Yitong Liu
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Bin Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Michael F Santillo
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Menghang Xia
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
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170
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS CENTRAL SCIENCE 2017; 3:143-147. [PMID: 28386587 PMCID: PMC5364449 DOI: 10.1021/acscentsci.7b00069] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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171
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Aitken L, Baillie G, Pannifer A, Morrison A, Jones PS, Smith TK, McElroy SP, Gunn-Moore FJ. In Vitro Assay Development and HTS of Small-Molecule Human ABAD/17β-HSD10 Inhibitors as Therapeutics in Alzheimer’s Disease. SLAS DISCOVERY 2017; 22:676-685. [DOI: 10.1177/2472555217697964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A major hallmark of Alzheimer’s disease (AD) is the formation of neurotoxic aggregates composed of the amyloid-β peptide (Aβ). Aβ has been recognized to interact with numerous proteins, resulting in pathological changes to the metabolism of patients with AD. One such mitochondrial metabolic enzyme is amyloid-binding alcohol dehydrogenase (ABAD), where altered enzyme function caused by the Aβ-ABAD interaction is known to cause mitochondrial distress and cytotoxic effects, providing a feasible therapeutic target for AD drug development. Here we have established a high-throughput screening platform for the identification of modulators to the ABAD enzyme. A pilot screen with a total of 6759 compounds from the NIH Clinical Collections (NCC) and SelleckChem libraries and a selection of compounds from the BioAscent diversity collection have allowed validation and robustness to be optimized. The pilot screen revealed 16 potential inhibitors in the low µM range against ABAD with favorable physicochemical properties for blood-brain barrier penetration.
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Affiliation(s)
- Laura Aitken
- School of Biology, University of St. Andrews, Medical and Biological Sciences Building, North Haugh, St. Andrews, Fife, UK
| | - Gemma Baillie
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, Lanarkshire, UK
| | - Andrew Pannifer
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, Lanarkshire, UK
| | - Angus Morrison
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, Lanarkshire, UK
| | - Philip S. Jones
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, Lanarkshire, UK
| | - Terry K. Smith
- Biomedical Sciences Research Complex, University of St. Andrews, Biomolecular Sciences Building, North Haugh, St. Andrews, Fife, UK
| | - Stuart P. McElroy
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, Lanarkshire, UK
| | - Frank J. Gunn-Moore
- School of Biology, University of St. Andrews, Medical and Biological Sciences Building, North Haugh, St. Andrews, Fife, UK
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172
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Chem Biol 2017; 12:575-578. [PMID: 28244728 DOI: 10.1021/acschembio.7b00119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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173
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Blevitt JM, Hack MD, Herman KL, Jackson PF, Krawczuk PJ, Lebsack AD, Liu AX, Mirzadegan T, Nelen MI, Patrick AN, Steinbacher S, Milla ME, Lumb KJ. Structural Basis of Small-Molecule Aggregate Induced Inhibition of a Protein-Protein Interaction. J Med Chem 2017; 60:3511-3517. [PMID: 28300404 DOI: 10.1021/acs.jmedchem.6b01836] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A prevalent observation in high-throughput screening and drug discovery programs is the inhibition of protein function by small-molecule compound aggregation. Here, we present the X-ray structural description of aggregation-based inhibition of a protein-protein interaction involving tumor necrosis factor α (TNFα). An ordered conglomerate of an aggregating small-molecule inhibitor (JNJ525) induces a quaternary structure switch of TNFα that inhibits the protein-protein interaction between TNFα and TNFα receptors. SPD-304 may employ a similar mechanism of inhibition.
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Affiliation(s)
- Jonathan M Blevitt
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Michael D Hack
- Lead Discovery, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Krystal L Herman
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Paul F Jackson
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Paul J Krawczuk
- Immunology, Janssen R&D LLC , Spring House, Pennsylvania 19477, United States
| | - Alec D Lebsack
- Immunology, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Annie X Liu
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , Spring House, Pennsylvania 19477, United States
| | - Taraneh Mirzadegan
- Lead Discovery, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Marina I Nelen
- Lead Discovery, Discovery Sciences, Janssen R&D LLC , Spring House, Pennsylvania 19477, United States
| | - Aaron N Patrick
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , Spring House, Pennsylvania 19477, United States
| | | | - Marcos E Milla
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Kevin J Lumb
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , Spring House, Pennsylvania 19477, United States
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174
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Chem Neurosci 2017; 8:420-423. [PMID: 28244737 DOI: 10.1021/acschemneuro.7b00064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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175
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. J Chem Inf Model 2017; 57:387-390. [PMID: 28244743 DOI: 10.1021/acs.jcim.7b00105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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176
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. Biochemistry 2017; 56:1363-1366. [PMID: 28244742 DOI: 10.1021/acs.biochem.7b00110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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177
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. J Med Chem 2017; 60:2165-2168. [PMID: 28244745 DOI: 10.1021/acs.jmedchem.7b00229] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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178
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Capuzzi SJ, Muratov EN, Tropsha A. Phantom PAINS: Problems with the Utility of Alerts for Pan-Assay INterference CompoundS. J Chem Inf Model 2017; 57:417-427. [PMID: 28165734 PMCID: PMC5411023 DOI: 10.1021/acs.jcim.6b00465] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of substructural alerts to identify Pan-Assay INterference compoundS (PAINS) has become a common component of the triage process in biological screening campaigns. These alerts, however, were originally derived from a proprietary library tested in just six assays measuring protein-protein interaction (PPI) inhibition using the AlphaScreen detection technology only; moreover, 68% (328 out of the 480 alerts) were derived from four or fewer compounds. In an effort to assess the reliability of these alerts as indicators of pan-assay interference, we performed a large-scale analysis of the impact of PAINS alerts on compound promiscuity in bioassays using publicly available data in PubChem. We found that the majority (97%) of all compounds containing PAINS alerts were actually infrequent hitters in AlphaScreen assays measuring PPI inhibition. We also found that the presence of PAINS alerts, contrary to expectations, did not reflect any heightened assay activity trends across all assays in PubChem including AlphaScreen, luciferase, beta-lactamase, or fluorescence-based assays. In addition, 109 PAINS alerts were present in 3570 extensively assayed, but consistently inactive compounds called Dark Chemical Matter. Finally, we observed that 87 small molecule FDA-approved drugs contained PAINS alerts and profiled their bioassay activity. Based on this detailed analysis of PAINS alerts in nonproprietary compound libraries, we caution against the blind use of PAINS filters to detect and triage compounds with possible PAINS liabilities and recommend that such conclusions should be drawn only by conducting orthogonal experiments.
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Affiliation(s)
- Stephen J Capuzzi
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
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179
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Tomohara K, Ito T, Onikata S, Kato A, Adachi I. Discovery of hyaluronidase inhibitors from natural products and their mechanistic characterization under DMSO-perturbed assay conditions. Bioorg Med Chem Lett 2017; 27:1620-1623. [PMID: 28202328 DOI: 10.1016/j.bmcl.2017.01.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 12/19/2022]
Abstract
The present study discovered four novel hyaluronan-degrading enzyme (hyaluronidase) inhibitors including chikusetsusaponins and catechins through the activity-guided separation of Panax japonicus and Prunus salicina, respectively. Although the discovery resulted in identification of usual frequent hitters, subsequent mechanistic characterizations under our DMSO-perturbed assay conditions and related protocols revealed that chikusetusaponin IV would serve as an aggregating and non-specific binding inhibitor, while (-)-epicatechin would interact specifically with enzyme at the catalytic site or more likely at a kind of catechin-binding site with a relatively week inhibitory activity. The latter description might provide a possible explanation for the well-known fact that a series of catechin have been described as frequent hitters in biological assays with a moderate activity. Thus, the present study demonstrated a practical and robust methodology to characterize initial screening hits mechanistically molecule-by-molecule in the early stage of natural product-based drug discovery.
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Affiliation(s)
- Keisuke Tomohara
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Tomohiro Ito
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Saika Onikata
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Atsushi Kato
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Isao Adachi
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
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180
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Abstract
The allure of phenotypic screening, combined with the industry preference for target-based approaches, has prompted the development of innovative chemical biology technologies that facilitate the identification of new therapeutic targets for accelerated drug discovery. A chemogenomic library is a collection of selective small-molecule pharmacological agents, and a hit from such a set in a phenotypic screen suggests that the annotated target or targets of that pharmacological agent may be involved in perturbing the observable phenotype. In this Review, we describe opportunities for chemogenomic screening to considerably expedite the conversion of phenotypic screening projects into target-based drug discovery approaches. Other applications are explored, including drug repositioning, predictive toxicology and the discovery of novel pharmacological modalities.
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181
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Yan X, Zheng Y, Gao J, Lee J. An Ink-jet Printing Strategy for Extensive Exploration of One Chemical Action with Three Interactive Variations. ANAL SCI 2017; 33:1-3. [PMID: 28070062 DOI: 10.2116/analsci.33.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A simple method was created and implemented through the technology of ink-jet printing to study the effects of three chemical factors (chemical reagents) to the ninhydrin reaction. The effects of each single reagent and their interactions on the reaction were studied in one experiment. The three reagents all have effects on ninhydrin reaction, and the effects under the different combinations of reagents were presented on a chip. This work was completed efficiently with a smaller experimental workload compared with the traditional method.
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Affiliation(s)
- Xing Yan
- College of Tourism and Environment, Shaanxi Normal University
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182
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Chen F, Sun H, Liu H, Li D, Li Y, Hou T. Prediction of luciferase inhibitors by the high-performance MIEC-GBDT approach based on interaction energetic patterns. Phys Chem Chem Phys 2017; 19:10163-10176. [DOI: 10.1039/c6cp08232g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The MIEC-GBDT model can be used as a powerful tool to identify potential interference compounds in luciferase-based high-throughput screening.
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Affiliation(s)
- Fu Chen
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Huiyong Sun
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Hui Liu
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Dan Li
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
- State Key Lab of CAD&CG
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183
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Shoombuatong W, Prathipati P, Owasirikul W, Worachartcheewan A, Simeon S, Anuwongcharoen N, Wikberg JES, Nantasenamat C. Towards the Revival of Interpretable QSAR Models. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2017. [DOI: 10.1007/978-3-319-56850-8_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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184
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Houck KA, Judson RS, Knudsen TB, Martin MT, Richard AM, Crofton KM, Simeonov A, Paules RS, Bucher JR, Thomas RS. Comment on "On the Utility of ToxCast™ and ToxPi as Methods for Identifying New Obesogens". ENVIRONMENTAL HEALTH PERSPECTIVES 2017; 125:A8-A11. [PMID: 28055944 PMCID: PMC5226707 DOI: 10.1289/ehp881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Keith A. Houck
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Richard S. Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Thomas B. Knudsen
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Matthew T. Martin
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Ann M. Richard
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Kevin M. Crofton
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Richard S. Paules
- National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - John R. Bucher
- National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Russell S. Thomas
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
- Address correspondence to R.S. Thomas, National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27705 USA. Telephone: 919-541-5776. E-mail:
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185
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Engen K, Rosenström U, Axelsson H, Konda V, Dahllund L, Otrocka M, Sigmundsson K, Nikolaou A, Vauquelin G, Hallberg M, Jenmalm Jensen A, Lundbäck T, Larhed M. Identification of Drug-Like Inhibitors of Insulin-Regulated Aminopeptidase Through Small-Molecule Screening. Assay Drug Dev Technol 2016; 14:180-93. [PMID: 27078680 DOI: 10.1089/adt.2016.708] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Intracerebroventricular injection of angiotensin IV, a ligand of insulin-regulated aminopeptidase (IRAP), has been shown to improve cognitive functions in several animal models. Consequently, IRAP is considered a potential target for treatment of cognitive disorders. To identify nonpeptidic IRAP inhibitors, we adapted an established enzymatic assay based on membrane preparations from Chinese hamster ovary cells and a synthetic peptide-like substrate for high-throughput screening purposes. The 384-well microplate-based absorbance assay was used to screen a diverse set of 10,500 compounds for their inhibitory capacity of IRAP. The assay performance was robust with Z'-values ranging from 0.81 to 0.91, and the screen resulted in 23 compounds that displayed greater than 60% inhibition at a compound concentration of 10 μM. After hit confirmation experiments, purity analysis, and promiscuity investigations, three structurally different compounds were considered particularly interesting as starting points for the development of small-molecule-based IRAP inhibitors. After resynthesis, all three compounds confirmed low μM activity and were shown to be rapidly reversible. Additional characterization included activity in a fluorescence-based orthogonal assay and in the presence of a nonionic detergent and a reducing agent, respectively. Importantly, the characterized compounds also showed inhibition of the human ortholog, prompting our further interest in these novel IRAP inhibitors.
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Affiliation(s)
- Karin Engen
- 1 Division of Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University , Uppsala, Sweden
| | - Ulrika Rosenström
- 1 Division of Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University , Uppsala, Sweden
| | - Hanna Axelsson
- 2 Chemical Biology Consortium Sweden, Science for Life Laboratory Stockholm, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Solna, Sweden
| | - Vivek Konda
- 1 Division of Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University , Uppsala, Sweden
| | - Leif Dahllund
- 3 Drug Discovery and Development Platform, Science for Life Laboratory Stockholm , Solna, Sweden
| | - Magdalena Otrocka
- 2 Chemical Biology Consortium Sweden, Science for Life Laboratory Stockholm, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Solna, Sweden
| | - Kristmundur Sigmundsson
- 2 Chemical Biology Consortium Sweden, Science for Life Laboratory Stockholm, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Solna, Sweden
| | - Alexandros Nikolaou
- 4 Department of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel , Brussels, Belgium
| | - Georges Vauquelin
- 4 Department of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel , Brussels, Belgium
| | - Mathias Hallberg
- 5 Beijer Laboratory, Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University , Uppsala, Sweden
| | - Annika Jenmalm Jensen
- 2 Chemical Biology Consortium Sweden, Science for Life Laboratory Stockholm, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Solna, Sweden
| | - Thomas Lundbäck
- 2 Chemical Biology Consortium Sweden, Science for Life Laboratory Stockholm, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Solna, Sweden
| | - Mats Larhed
- 6 Science for Life Laboratory Uppsala, Division of Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University , Uppsala, Sweden
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186
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Kleinstreuer NC, Ceger P, Watt ED, Martin M, Houck K, Browne P, Thomas RS, Casey WM, Dix DJ, Allen D, Sakamuru S, Xia M, Huang R, Judson R. Development and Validation of a Computational Model for Androgen Receptor Activity. Chem Res Toxicol 2016; 30:946-964. [PMID: 27933809 PMCID: PMC5396026 DOI: 10.1021/acs.chemrestox.6b00347] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Testing thousands of chemicals to identify potential androgen receptor (AR) agonists or antagonists would cost millions of dollars and take decades to complete using current validated methods. High-throughput in vitro screening (HTS) and computational toxicology approaches can more rapidly and inexpensively identify potential androgen-active chemicals. We integrated 11 HTS ToxCast/Tox21 in vitro assays into a computational network model to distinguish true AR pathway activity from technology-specific assay interference. The in vitro HTS assays probed perturbations of the AR pathway at multiple points (receptor binding, coregulator recruitment, gene transcription, and protein production) and multiple cell types. Confirmatory in vitro antagonist assay data and cytotoxicity information were used as additional flags for potential nonspecific activity. Validating such alternative testing strategies requires high-quality reference data. We compiled 158 putative androgen-active and -inactive chemicals from a combination of international test method validation efforts and semiautomated systematic literature reviews. Detailed in vitro assay information and results were compiled into a single database using a standardized ontology. Reference chemical concentrations that activated or inhibited AR pathway activity were identified to establish a range of potencies with reproducible reference chemical results. Comparison with existing Tier 1 AR binding data from the U.S. EPA Endocrine Disruptor Screening Program revealed that the model identified binders at relevant test concentrations (<100 μM) and was more sensitive to antagonist activity. The AR pathway model based on the ToxCast/Tox21 assays had balanced accuracies of 95.2% for agonist (n = 29) and 97.5% for antagonist (n = 28) reference chemicals. Out of 1855 chemicals screened in the AR pathway model, 220 chemicals demonstrated AR agonist or antagonist activity and an additional 174 chemicals were predicted to have potential weak AR pathway activity.
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Affiliation(s)
- Nicole C Kleinstreuer
- NIH/NIEHS/DNTP/The NTP Interagency Center for the Evaluation of Alternative Toxicological Methods , Research Triangle Park, North Carolina 27713, United States
| | - Patricia Ceger
- Integrated Laboratory Systems, Inc. , Research Triangle Park, North Carolina 27560, United States
| | - Eric D Watt
- EPA/ORD/National Center for Computational Toxicology , Research Triangle Park, North Carolina 27711, United States
| | - Matthew Martin
- EPA/ORD/National Center for Computational Toxicology , Research Triangle Park, North Carolina 27711, United States
| | - Keith Houck
- EPA/ORD/National Center for Computational Toxicology , Research Triangle Park, North Carolina 27711, United States
| | - Patience Browne
- OECD Environment Directorate, Environment Health and Safety Division , Paris 75775, France
| | - Russell S Thomas
- EPA/ORD/National Center for Computational Toxicology , Research Triangle Park, North Carolina 27711, United States
| | - Warren M Casey
- NIH/NIEHS/DNTP/The NTP Interagency Center for the Evaluation of Alternative Toxicological Methods , Research Triangle Park, North Carolina 27713, United States
| | - David J Dix
- EPA/OCSPP/Office of Science Coordination and Policy , Washington, DC, 20460, United States
| | - David Allen
- Integrated Laboratory Systems, Inc. , Research Triangle Park, North Carolina 27560, United States
| | - Srilatha Sakamuru
- NIH/National Center for Advancing Translational Sciences , Bethesda, Maryland 20892, United States
| | - Menghang Xia
- NIH/National Center for Advancing Translational Sciences , Bethesda, Maryland 20892, United States
| | - Ruili Huang
- NIH/National Center for Advancing Translational Sciences , Bethesda, Maryland 20892, United States
| | - Richard Judson
- EPA/ORD/National Center for Computational Toxicology , Research Triangle Park, North Carolina 27711, United States
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187
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Jang DS, Ye W, Guimei T, Solomon M, Southall N, Hu X, Marugan J, Ferrer M, Maegawa GHB. Cell-based high-throughput screening identifies galactocerebrosidase enhancers as potential small-molecule therapies for Krabbe's disease. J Neurosci Res 2016; 94:1231-45. [PMID: 27638606 PMCID: PMC5328637 DOI: 10.1002/jnr.23875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/01/2016] [Accepted: 07/14/2016] [Indexed: 11/08/2022]
Abstract
Krabbe's disease, also known as globoid cell leukodystrophy (GLD), is a lysosomal storage disease caused by the deficiency of the lysosomal enzyme β-galactocerebrosidase (GALC), resulting in severe neurological manifestations related to demyelination secondary to elevated galactosylsphingosine (psychosine) with its subsequent cytotoxicity. The only available treatment is hematopoietic stem cell transplantation, which delays disease onset but does not prevent long-term neurological manifestations. This article describes the identification of small molecules that enhance mutant GALC activity, identified by quantitative cell-based high-throughput screening (qHTS). Using a specific neurologically relevant murine cell line (145M-Twi) modified to express common human hGALC-G270D mutant, we were able to detect GALC activity in a 1,536-well microplate format. The qHTS of approximately 46,000 compounds identified three small molecules that showed significant enhancements of residual mutant GALC activity in primary cell lines from GLD patients. These compounds were shown to increase the levels of GALC-G270D mutant in the lysosomal compartment. In kinetic assessments, these small molecules failed to disturb the GALC kinetic profile under acidic conditions, which is highly desirable for folding-assisting molecules operating in the endoplasmic reticulum and not affecting GALC catalytic properties in the lysosomal compartment. In addition, these small molecules rescued the decreased GALC activity at neutral pH and partially stabilized GALC under heat-denaturating conditions. These drug-like compounds can be used as the starting point to develop novel small-molecule agents to treat the progressive neurodegenerative course of GLD. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Dae Song Jang
- Department of Pediatrics, University of Florida, Gainesville, Florida
| | - Wenjuan Ye
- National Institutes of Health Center for Advancing Translational Sciences, Rockville, Maryland
| | - Tian Guimei
- Department of Pediatrics, University of Florida, Gainesville, Florida
| | - Melani Solomon
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Noel Southall
- National Institutes of Health Center for Advancing Translational Sciences, Rockville, Maryland
| | - Xin Hu
- National Institutes of Health Center for Advancing Translational Sciences, Rockville, Maryland
| | - Juan Marugan
- National Institutes of Health Center for Advancing Translational Sciences, Rockville, Maryland
| | - Marc Ferrer
- National Institutes of Health Center for Advancing Translational Sciences, Rockville, Maryland
| | - Gustavo H B Maegawa
- Department of Pediatrics, University of Florida, Gainesville, Florida.
- Department of Neuroscience, University of Florida, Gainesville, Florida.
- Department of Microbiology and Immunology, University of Florida, Gainesville, Florida.
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188
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Williamson AE, Ylioja PM, Robertson MN, Antonova-Koch Y, Avery V, Baell JB, Batchu H, Batra S, Burrows JN, Bhattacharyya S, Calderon F, Charman SA, Clark J, Crespo B, Dean M, Debbert SL, Delves M, Dennis ASM, Deroose F, Duffy S, Fletcher S, Giaever G, Hallyburton I, Gamo FJ, Gebbia M, Guy RK, Hungerford Z, Kirk K, Lafuente-Monasterio M, Lee A, Meister S, Nislow C, Overington JP, Papadatos G, Patiny L, Pham J, Ralph S, Ruecker A, Ryan E, Southan C, Srivastava K, Swain C, Tarnowski M, Thomson P, Turner P, Wallace IM, Wells TC, White K, White L, Willis P, Winzeler EA, Wittlin S, Todd MH. Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles. ACS CENTRAL SCIENCE 2016; 2:687-701. [PMID: 27800551 PMCID: PMC5084075 DOI: 10.1021/acscentsci.6b00086] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Indexed: 05/26/2023]
Abstract
The development of new antimalarial compounds remains a pivotal part of the strategy for malaria elimination. Recent large-scale phenotypic screens have provided a wealth of potential starting points for hit-to-lead campaigns. One such public set is explored, employing an open source research mechanism in which all data and ideas were shared in real time, anyone was able to participate, and patents were not sought. One chemical subseries was found to exhibit oral activity but contained a labile ester that could not be replaced without loss of activity, and the original hit exhibited remarkable sensitivity to minor structural change. A second subseries displayed high potency, including activity within gametocyte and liver stage assays, but at the cost of low solubility. As an open source research project, unexplored avenues are clearly identified and may be explored further by the community; new findings may be cumulatively added to the present work.
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Affiliation(s)
- Alice E. Williamson
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paul M. Ylioja
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Murray N. Robertson
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Yevgeniya Antonova-Koch
- Department
of Pediatrics, Pharmacology & Drug Development, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Vicky Avery
- Discovery Biology, Eskitis Institute for
Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Jonathan B. Baell
- Monash
Institute of Pharmaceutical Sciences, Monash
University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Harikrishna Batchu
- CSIR-Central
Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226 031, India
| | - Sanjay Batra
- CSIR-Central
Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226 031, India
| | - Jeremy N. Burrows
- Medicines for Malaria Venture, PO Box
1826, 20 rte de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Soumya Bhattacharyya
- CSIR-Central
Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226 031, India
| | - Felix Calderon
- Tres Cantos Medicines Development Campus, Diseases of the Developing
World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Susan A. Charman
- Monash
Institute of Pharmaceutical Sciences, Monash
University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Julie Clark
- Department of Chemical
Biology & Therapeutics, St. Jude Children’s
Research Hospital, MS 1000, Room E9050, 262 Danny Thomas Place, Memphis, Tennessee 38105-3678, United States
| | - Benigno Crespo
- Tres Cantos Medicines Development Campus, Diseases of the Developing
World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Matin Dean
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Stefan L. Debbert
- Department of Chemistry, Lawrence University, 233 Steitz Science
Hall, 711 East Boldt Way, Appleton, Wisconsin 54911, United States
| | - Michael Delves
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, U.K.
| | - Adelaide S. M. Dennis
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Frederik Deroose
- Asclepia Outsourcing Solutions, Damvalleistraat 49, B-9070 Destelbergen, Belgium
| | - Sandra Duffy
- Discovery Biology, Eskitis Institute for
Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Sabine Fletcher
- Discovery Biology, Eskitis Institute for
Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Guri Giaever
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Irene Hallyburton
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, University
of Dundee, Dundee, DD1 5EH, U.K.
| | - Francisco-Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing
World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Marinella Gebbia
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - R. Kiplin Guy
- Department of Chemical
Biology & Therapeutics, St. Jude Children’s
Research Hospital, MS 1000, Room E9050, 262 Danny Thomas Place, Memphis, Tennessee 38105-3678, United States
| | - Zoe Hungerford
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Kiaran Kirk
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Maria
J. Lafuente-Monasterio
- Tres Cantos Medicines Development Campus, Diseases of the Developing
World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Anna Lee
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Stephan Meister
- Department
of Pediatrics, Pharmacology & Drug Development, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Corey Nislow
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - John P. Overington
- European Molecular
Biology Laboratory—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, U.K.
| | - George Papadatos
- European Molecular
Biology Laboratory—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, U.K.
| | - Luc Patiny
- Institute of Chemical Sciences and Engineering
(ISIC), Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - James Pham
- Department
of Biochemistry & Molecular Biology, Bio21 Molecular Science and
Biotechnology Institute, The University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Stuart
A. Ralph
- Department
of Biochemistry & Molecular Biology, Bio21 Molecular Science and
Biotechnology Institute, The University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Andrea Ruecker
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, U.K.
| | - Eileen Ryan
- Monash
Institute of Pharmaceutical Sciences, Monash
University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Christopher Southan
- IUPHAR/BPS Guide to PHARMACOLOGY, Centre for Integrative Physiology,
School of Biomedical Sciences, University
of Edinburgh, Edinburgh, EH8 9XD, U.K.
| | - Kumkum Srivastava
- CSIR-Central
Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226 031, India
| | - Chris Swain
- Cambridge MedChem
Consulting, 8 Mangers
Lane, Duxford, Cambridge CB22 4RN, U.K.
| | - Matthew
J. Tarnowski
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Patrick Thomson
- School
of Chemistry, The University of Edinburgh, Joseph Black Building, West Mains
Road, Edinburgh EH9 3JJ, U.K.
| | - Peter Turner
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Iain M. Wallace
- European Molecular
Biology Laboratory—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, U.K.
| | - Timothy
N. C. Wells
- Medicines for Malaria Venture, PO Box
1826, 20 rte de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Karen White
- Monash
Institute of Pharmaceutical Sciences, Monash
University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Laura White
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paul Willis
- Medicines for Malaria Venture, PO Box
1826, 20 rte de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Elizabeth A. Winzeler
- Department
of Pediatrics, Pharmacology & Drug Development, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
| | - Matthew H. Todd
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
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189
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Dietz BM, Hajirahimkhan A, Dunlap TL, Bolton JL. Botanicals and Their Bioactive Phytochemicals for Women's Health. Pharmacol Rev 2016; 68:1026-1073. [PMID: 27677719 PMCID: PMC5050441 DOI: 10.1124/pr.115.010843] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Botanical dietary supplements are increasingly popular for women's health, particularly for older women. The specific botanicals women take vary as a function of age. Younger women will use botanicals for urinary tract infections, especially Vaccinium macrocarpon (cranberry), where there is evidence for efficacy. Botanical dietary supplements for premenstrual syndrome (PMS) are less commonly used, and rigorous clinical trials have not been done. Some examples include Vitex agnus-castus (chasteberry), Angelica sinensis (dong quai), Viburnum opulus/prunifolium (cramp bark and black haw), and Zingiber officinale (ginger). Pregnant women have also used ginger for relief from nausea. Natural galactagogues for lactating women include Trigonella foenum-graecum (fenugreek) and Silybum marianum (milk thistle); however, rigorous safety and efficacy studies are lacking. Older women suffering menopausal symptoms are increasingly likely to use botanicals, especially since the Women's Health Initiative showed an increased risk for breast cancer associated with traditional hormone therapy. Serotonergic mechanisms similar to antidepressants have been proposed for Actaea/Cimicifuga racemosa (black cohosh) and Valeriana officinalis (valerian). Plant extracts with estrogenic activities for menopausal symptom relief include Glycine max (soy), Trifolium pratense (red clover), Pueraria lobata (kudzu), Humulus lupulus (hops), Glycyrrhiza species (licorice), Rheum rhaponticum (rhubarb), Vitex agnus-castus (chasteberry), Linum usitatissimum (flaxseed), Epimedium species (herba Epimedii, horny goat weed), and Medicago sativa (alfalfa). Some of the estrogenic botanicals have also been shown to have protective effects against osteoporosis. Several of these botanicals could have additional breast cancer preventive effects linked to hormonal, chemical, inflammatory, and/or epigenetic pathways. Finally, although botanicals are perceived as natural safe remedies, it is important for women and their healthcare providers to realize that they have not been rigorously tested for potential toxic effects and/or drug/botanical interactions. Understanding the mechanism of action of these supplements used for women's health will ultimately lead to standardized botanical products with higher efficacy, safety, and chemopreventive properties.
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Affiliation(s)
- Birgit M Dietz
- University of Illinois at Chicago/National Institutes of Health Center for Botanical Dietary Supplements, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Atieh Hajirahimkhan
- University of Illinois at Chicago/National Institutes of Health Center for Botanical Dietary Supplements, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Tareisha L Dunlap
- University of Illinois at Chicago/National Institutes of Health Center for Botanical Dietary Supplements, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Judy L Bolton
- University of Illinois at Chicago/National Institutes of Health Center for Botanical Dietary Supplements, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
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190
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Rabelo VW, Santos TF, Terra L, Santana MV, Castro HC, Rodrigues CR, Abreu PA. Targeting CYP51 for drug design by the contributions of molecular modeling. Fundam Clin Pharmacol 2016; 31:37-53. [PMID: 27487199 DOI: 10.1111/fcp.12230] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/15/2016] [Accepted: 08/01/2016] [Indexed: 11/28/2022]
Abstract
CYP51 is an enzyme of sterol biosynthesis pathway present in animals, plants, protozoa and fungi. This enzyme is described as an important drug target that is still of interest. Therefore, in this work, we reviewed the structure and function of CYP51 and explored the molecular modeling approaches for the development of new antifungal and antiprotozoans that target this enzyme. Crystallographic structures of CYP51 of some organisms have already been described in the literature, which enable the construction of homology models of other organisms' enzymes and molecular docking studies of new ligands. The binding mode and interactions of some new series of azoles with antifungal or antiprotozoan activities has been studied and showed important residues of the active site. Molecular modeling is an important tool to be explored for the discovery and optimization of CYP51 inhibitors with better activities, pharmacokinetics, and toxicological profiles.
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Affiliation(s)
- Vitor W Rabelo
- Laboratório de Modelagem Molecular e Pesquisa em Ciências Farmacêuticas (LAMCIFAR), Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Avenida São José do Barreto 767, CEP 27965-045, Macaé, RJ, Brazil
| | - Taísa F Santos
- Laboratório de Modelagem Molecular e Pesquisa em Ciências Farmacêuticas (LAMCIFAR), Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Avenida São José do Barreto 767, CEP 27965-045, Macaé, RJ, Brazil
| | - Luciana Terra
- Laboratório de Antibióticos, Bioquímica, Ensino e Modelagem Molecular (LabiEMol), Instituto de Biologia, Universidade Federal Fluminense, Campus Valonguinho Outeiro de São João Baptista s/n, Centro, CEP 24210130, Niterói, RJ, Brazil
| | - Marcos V Santana
- Laboratório de Antibióticos, Bioquímica, Ensino e Modelagem Molecular (LabiEMol), Instituto de Biologia, Universidade Federal Fluminense, Campus Valonguinho Outeiro de São João Baptista s/n, Centro, CEP 24210130, Niterói, RJ, Brazil
| | - Helena C Castro
- Laboratório de Antibióticos, Bioquímica, Ensino e Modelagem Molecular (LabiEMol), Instituto de Biologia, Universidade Federal Fluminense, Campus Valonguinho Outeiro de São João Baptista s/n, Centro, CEP 24210130, Niterói, RJ, Brazil
| | - Carlos R Rodrigues
- Laboratório de Modelagem Molecular e QSAR (ModMolQSAR), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, CEP 21941-599, Rio de Janeiro, RJ, Brazil
| | - Paula A Abreu
- Laboratório de Modelagem Molecular e Pesquisa em Ciências Farmacêuticas (LAMCIFAR), Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Avenida São José do Barreto 767, CEP 27965-045, Macaé, RJ, Brazil
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191
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Ulanday GEL, Okamoto K, Morita K. Development and utility of an in vitro, fluorescence-based assay for the discovery of novel compounds against dengue 2 viral protease. Trop Med Health 2016; 44:22. [PMID: 27551237 PMCID: PMC4979183 DOI: 10.1186/s41182-016-0025-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/18/2016] [Indexed: 11/27/2022] Open
Abstract
Background Dengue disease is one of the most significant vector-borne illnesses in the world. The emergence and re-emergence of dengue infections in many parts of the world affect millions annually and continue to burden public health systems especially in low-income populations. Advances in dengue vaccine development showed promising results; however, protection seems to be suboptimal. There is no licensed chemotherapeutic agent against dengue to date. An ideal scenario of combinatorial vaccination of high-risk individuals and chemotherapy of the diseased during outbreaks may compensate for the meager protection offered by the vaccine. The dengue virus protease is important to viral replication and, as such, has been identified as a potential target for antivirals. It is, therefore, our objective to establish and optimize an appropriate screening method for use during the early stages of drug development for dengue. Methods In this study, we developed and optimized a biochemical assay system for use in screening compound libraries against dengue virus protease. We tested the selected protease inhibitors with a cell-based assay to determine inhibition of viral replication. Results We have presented direct plots of substrate kinetics data showing an apparent inhibition of the protease at excessive substrate concentrations. The most common sources of interference that may have affected the said observation were elucidated. Finally, a screen was done on an existing compound library using the developed method. The compounds selected in this study showed inhibitory activity against both the recombinant dengue protease and cell-based infectivity assays. Conclusions Our study shows the practicality of a customized biochemical assay to find possible inhibitors of dengue viral protease during the initial stages of drug discovery. Electronic supplementary material The online version of this article (doi:10.1186/s41182-016-0025-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gianne Eduard L Ulanday
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan ; Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kenta Okamoto
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan ; Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan ; Leading Graduate School Program, Nagasaki University, Nagasaki, Japan
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192
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Richard AM, Judson RS, Houck KA, Grulke CM, Volarath P, Thillainadarajah I, Yang C, Rathman J, Martin MT, Wambaugh JF, Knudsen TB, Kancherla J, Mansouri K, Patlewicz G, Williams AJ, Little SB, Crofton KM, Thomas RS. ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology. Chem Res Toxicol 2016; 29:1225-51. [PMID: 27367298 DOI: 10.1021/acs.chemrestox.6b00135] [Citation(s) in RCA: 386] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The U.S. Environmental Protection Agency's (EPA) ToxCast program is testing a large library of Agency-relevant chemicals using in vitro high-throughput screening (HTS) approaches to support the development of improved toxicity prediction models. Launched in 2007, Phase I of the program screened 310 chemicals, mostly pesticides, across hundreds of ToxCast assay end points. In Phase II, the ToxCast library was expanded to 1878 chemicals, culminating in the public release of screening data at the end of 2013. Subsequent expansion in Phase III has resulted in more than 3800 chemicals actively undergoing ToxCast screening, 96% of which are also being screened in the multi-Agency Tox21 project. The chemical library unpinning these efforts plays a central role in defining the scope and potential application of ToxCast HTS results. The history of the phased construction of EPA's ToxCast library is reviewed, followed by a survey of the library contents from several different vantage points. CAS Registry Numbers are used to assess ToxCast library coverage of important toxicity, regulatory, and exposure inventories. Structure-based representations of ToxCast chemicals are then used to compute physicochemical properties, substructural features, and structural alerts for toxicity and biotransformation. Cheminformatics approaches using these varied representations are applied to defining the boundaries of HTS testability, evaluating chemical diversity, and comparing the ToxCast library to potential target application inventories, such as used in EPA's Endocrine Disruption Screening Program (EDSP). Through several examples, the ToxCast chemical library is demonstrated to provide comprehensive coverage of the knowledge domains and target inventories of potential interest to EPA. Furthermore, the varied representations and approaches presented here define local chemistry domains potentially worthy of further investigation (e.g., not currently covered in the testing library or defined by toxicity "alerts") to strategically support data mining and predictive toxicology modeling moving forward.
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Affiliation(s)
- Ann M Richard
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Richard S Judson
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Keith A Houck
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Christopher M Grulke
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Patra Volarath
- Center for Food Safety and Nutrition, U.S. Food and Drug Administration , 5100 Paint Branch Parkway, College Park, Maryland 20740, United States
| | - Inthirany Thillainadarajah
- Senior Environmental Employment Program, U.S. Environmental Protection Agency , Research Triangle Park, Durham, North Carolina 27711, United States
| | - Chihae Yang
- Molecular Networks GmbH , Henkestraße 91, 91052 Erlangen, Germany.,Altamira, LLC , 1455 Candlewood Drive, Columbus, Ohio 43235, United States
| | - James Rathman
- Altamira, LLC , 1455 Candlewood Drive, Columbus, Ohio 43235, United States.,Department of Chemical and Biomolecular Engineering, The Ohio State University , 151 W. Woodruff Avenue, Columbus, Ohio 43210, United States
| | - Matthew T Martin
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - John F Wambaugh
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Thomas B Knudsen
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Jayaram Kancherla
- ORISE Fellow, U.S. Environmental Protection Agency, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Kamel Mansouri
- ORISE Fellow, U.S. Environmental Protection Agency, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Grace Patlewicz
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Antony J Williams
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Stephen B Little
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Kevin M Crofton
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Russell S Thomas
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
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193
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Interpreting the behavior of concentration–response curves of hyaluronidase inhibitors under DMSO-perturbed assay conditions. Bioorg Med Chem Lett 2016; 26:3153-3157. [DOI: 10.1016/j.bmcl.2016.04.082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 04/26/2016] [Accepted: 04/28/2016] [Indexed: 11/22/2022]
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194
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Judson R, Houck K, Martin M, Richard AM, Knudsen TB, Shah I, Little S, Wambaugh J, Woodrow Setzer R, Kothiya P, Phuong J, Filer D, Smith D, Reif D, Rotroff D, Kleinstreuer N, Sipes N, Xia M, Huang R, Crofton K, Thomas RS. Editor's Highlight: Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space. Toxicol Sci 2016; 152:323-39. [PMID: 27208079 DOI: 10.1093/toxsci/kfw092] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Chemical toxicity can arise from disruption of specific biomolecular functions or through more generalized cell stress and cytotoxicity-mediated processes. Here, responses of 1060 chemicals including pharmaceuticals, natural products, pesticidals, consumer, and industrial chemicals across a battery of 815 in vitro assay endpoints from 7 high-throughput assay technology platforms were analyzed in order to distinguish between these types of activities. Both cell-based and cell-free assays showed a rapid increase in the frequency of responses at concentrations where cell stress/cytotoxicity responses were observed in cell-based assays. Chemicals that were positive on at least 2 viability/cytotoxicity assays within the concentration range tested (typically up to 100 μM) activated a median of 12% of assay endpoints whereas those that were not cytotoxic in this concentration range activated 1.3% of the assays endpoints. The results suggest that activity can be broadly divided into: (1) specific biomolecular interactions against one or more targets (eg, receptors or enzymes) at concentrations below which overt cytotoxicity-associated activity is observed; and (2) activity associated with cell stress or cytotoxicity, which may result from triggering specific cell stress pathways, chemical reactivity, physico-chemical disruption of proteins or membranes, or broad low-affinity non-covalent interactions. Chemicals showing a greater number of specific biomolecular interactions are generally designed to be bioactive (pharmaceuticals or pesticidal active ingredients), whereas intentional food-use chemicals tended to show the fewest specific interactions. The analyses presented here provide context for use of these data in ongoing studies to predict in vivo toxicity from chemicals lacking extensive hazard assessment.
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Affiliation(s)
- Richard Judson
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina;
| | - Keith Houck
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Matt Martin
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Ann M Richard
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Thomas B Knudsen
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Imran Shah
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Stephen Little
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - John Wambaugh
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - R Woodrow Setzer
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Parth Kothiya
- Contractor to the U.S. EPA National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Jimmy Phuong
- Contractor to the U.S. EPA National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Dayne Filer
- ORISE Fellow at the U.S. EPA National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Doris Smith
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - David Reif
- Department of Statistics, North Carolina State University, Raleigh, North Carolina
| | - Daniel Rotroff
- Department of Statistics, North Carolina State University, Raleigh, North Carolina
| | | | - Nisha Sipes
- National Toxicology Program, Research Triangle Park, North Carolina
| | - Menghang Xia
- NIH National Center for Advancing Translational Sciences, Rockville, Maryland
| | - Ruili Huang
- NIH National Center for Advancing Translational Sciences, Rockville, Maryland
| | - Kevin Crofton
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Russell S Thomas
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
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195
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McLaughlin CK, Duan D, Ganesh AN, Torosyan H, Shoichet BK, Shoichet MS. Stable Colloidal Drug Aggregates Catch and Release Active Enzymes. ACS Chem Biol 2016; 11:992-1000. [PMID: 26741163 DOI: 10.1021/acschembio.5b00806] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Small molecule aggregates are considered nuisance compounds in drug discovery, but their unusual properties as colloids could be exploited to form stable vehicles to preserve protein activity. We investigated the coaggregation of seven molecules chosen because they had been previously intensely studied as colloidal aggregators, coformulating them with bis-azo dyes. The coformulation reduced colloid sizes to <100 nm and improved uniformity of the particle size distribution. The new colloid formulations are more stable than previous aggregator particles. Specifically, coaggregation of Congo Red with sorafenib, tetraiodophenolphthalein (TIPT), or vemurafenib produced particles that are stable in solutions of high ionic strength and high protein concentrations. Like traditional, single compound colloidal aggregates, the stabilized colloids adsorbed and inhibited enzymes like β-lactamase, malate dehydrogenase, and trypsin. Unlike traditional aggregates, the coformulated colloid-protein particles could be centrifuged and resuspended multiple times, and from resuspended particles, active trypsin could be released up to 72 h after adsorption. Unexpectedly, the stable colloidal formulations can sequester, stabilize, and isolate enzymes by spin-down, resuspension, and release.
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Affiliation(s)
- Christopher K. McLaughlin
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Da Duan
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
| | - Ahil N. Ganesh
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Hayarpi Torosyan
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
| | - Brian K. Shoichet
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
| | - Molly S. Shoichet
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
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196
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Thorne N, Malik N, Shah S, Zhao J, Class B, Aguisanda F, Southall N, Xia M, McKew JC, Rao M, Zheng W. High-Throughput Phenotypic Screening of Human Astrocytes to Identify Compounds That Protect Against Oxidative Stress. Stem Cells Transl Med 2016; 5:613-27. [PMID: 27034412 PMCID: PMC4835244 DOI: 10.5966/sctm.2015-0170] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 01/14/2016] [Indexed: 01/17/2023] Open
Abstract
UNLABELLED Astrocytes are the predominant cell type in the nervous system and play a significant role in maintaining neuronal health and homeostasis. Recently, astrocyte dysfunction has been implicated in the pathogenesis of many neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. Astrocytes are thus an attractive new target for drug discovery for neurological disorders. Using astrocytes differentiated from human embryonic stem cells, we have developed an assay to identify compounds that protect against oxidative stress, a condition associated with many neurodegenerative diseases. This phenotypic oxidative stress assay has been optimized for high-throughput screening in a 1,536-well plate format. From a screen of approximately 4,100 bioactive tool compounds and approved drugs, we identified a set of 22 that acutely protect human astrocytes from the consequences of hydrogen peroxide-induced oxidative stress. Nine of these compounds were also found to be protective of induced pluripotent stem cell-differentiated astrocytes in a related assay. These compounds are thought to confer protection through hormesis, activating stress-response pathways and preconditioning astrocytes to handle subsequent exposure to hydrogen peroxide. In fact, four of these compounds were found to activate the antioxidant response element/nuclear factor-E2-related factor 2 pathway, a protective pathway induced by toxic insults. Our results demonstrate the relevancy and utility of using astrocytes differentiated from human stem cells as a disease model for drug discovery and development. SIGNIFICANCE Astrocytes play a key role in neurological diseases. Drug discovery efforts that target astrocytes can identify novel therapeutics. Human astrocytes are difficult to obtain and thus are challenging to use for high-throughput screening, which requires large numbers of cells. Using human embryonic stem cell-derived astrocytes and an optimized astrocyte differentiation protocol, it was possible to screen approximately 4,100 compounds in titration to identify 22 that are cytoprotective of astrocytes. This study is the largest-scale high-throughput screen conducted using human astrocytes, with a total of 17,536 data points collected in the primary screen. The results demonstrate the relevancy and utility of using astrocytes differentiated from human stem cells as a disease model for drug discovery and development.
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Affiliation(s)
- Natasha Thorne
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Nasir Malik
- Laboratory of Stem Cell Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sonia Shah
- Laboratory of Stem Cell Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jean Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Bradley Class
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Francis Aguisanda
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - John C McKew
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Mahendra Rao
- NIH Center for Regenerative Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
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197
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Abstract
It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years.
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Affiliation(s)
- John J Irwin
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
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198
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Paul Friedman K, Watt ED, Hornung MW, Hedge JM, Judson RS, Crofton KM, Houck KA, Simmons SO. Tiered High-Throughput Screening Approach to Identify Thyroperoxidase Inhibitors Within the ToxCast Phase I and II Chemical Libraries. Toxicol Sci 2016; 151:160-80. [PMID: 26884060 DOI: 10.1093/toxsci/kfw034] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
High-throughput screening for potential thyroid-disrupting chemicals requires a system of assays to capture multiple molecular-initiating events (MIEs) that converge on perturbed thyroid hormone (TH) homeostasis. Screening for MIEs specific to TH-disrupting pathways is limited in the U.S. Environmental Protection Agency ToxCast screening assay portfolio. To fill 1 critical screening gap, the Amplex UltraRed-thyroperoxidase (AUR-TPO) assay was developed to identify chemicals that inhibit TPO, as decreased TPO activity reduces TH synthesis. The ToxCast phase I and II chemical libraries, comprised of 1074 unique chemicals, were initially screened using a single, high concentration to identify potential TPO inhibitors. Chemicals positive in the single-concentration screen were retested in concentration-response. Due to high false-positive rates typically observed with loss-of-signal assays such as AUR-TPO, we also employed 2 additional assays in parallel to identify possible sources of nonspecific assay signal loss, enabling stratification of roughly 300 putative TPO inhibitors based upon selective AUR-TPO activity. A cell-free luciferase inhibition assay was used to identify nonspecific enzyme inhibition among the putative TPO inhibitors, and a cytotoxicity assay using a human cell line was used to estimate the cellular tolerance limit. Additionally, the TPO inhibition activities of 150 chemicals were compared between the AUR-TPO and an orthogonal peroxidase oxidation assay using guaiacol as a substrate to confirm the activity profiles of putative TPO inhibitors. This effort represents the most extensive TPO inhibition screening campaign to date and illustrates a tiered screening approach that focuses resources, maximizes assay throughput, and reduces animal use.
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Affiliation(s)
- Katie Paul Friedman
- *Oak Ridge Institute for Science Education Postdoctoral Fellow, Oak Ridge, TN, 37831 Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711
| | - Eric D Watt
- *Oak Ridge Institute for Science Education Postdoctoral Fellow, Oak Ridge, TN, 37831 National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711
| | - Michael W Hornung
- Mid-Continent Ecology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Duluth, MN, 55804
| | - Joan M Hedge
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711
| | - Richard S Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711
| | - Kevin M Crofton
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711
| | - Keith A Houck
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711
| | - Steven O Simmons
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711,
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199
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Bernstock JD, Lee YJ, Peruzzotti-Jametti L, Southall N, Johnson KR, Maric D, Volpe G, Kouznetsova J, Zheng W, Pluchino S, Hallenbeck JM. A novel quantitative high-throughput screen identifies drugs that both activate SUMO conjugation via the inhibition of microRNAs 182 and 183 and facilitate neuroprotection in a model of oxygen and glucose deprivation. J Cereb Blood Flow Metab 2016; 36:426-41. [PMID: 26661196 PMCID: PMC4759677 DOI: 10.1177/0271678x15609939] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 08/05/2015] [Accepted: 08/27/2015] [Indexed: 01/06/2023]
Abstract
The conjugation/de-conjugation of Small Ubiquitin-like Modifier (SUMO) has been shown to be associated with a diverse set of physiologic/pathologic conditions. The clinical significance and ostensible therapeutic utility offered via the selective control of the global SUMOylation process has become readily apparent in ischemic pathophysiology. Herein, we describe the development of a novel quantitative high-throughput screening (qHTS) system designed to identify small molecules capable of increasing SUMOylation via the regulation/inhibition of members of the microRNA (miRNA)-182 family. This assay employs a SHSY5Y human neuroblastoma cell line stably transfected with a dual firefly-Renilla luciferase reporter system for identification of specific inhibitors of either miR-182 or miR-183. In this study, we have identified small molecules capable of inducing increased global conjugation of SUMO in both SHSY5Y cells and rat E18-derived primary cortical neurons. The protective effects of a number of the identified compounds were confirmed via an in vitro ischemic model (oxygen/glucose deprivation). Of note, this assay can be easily repurposed to allow high-throughput analyses of the potential drugability of other relevant miRNA(s) in ischemic pathobiology.
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Affiliation(s)
- Joshua D Bernstock
- Stroke Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NINDS/NIH), Bethesda, MD, USA Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Yang-ja Lee
- Stroke Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NINDS/NIH), Bethesda, MD, USA
| | - Luca Peruzzotti-Jametti
- Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health (NCATS/NIH), Bethesda, MD, USA
| | - Kory R Johnson
- Bioinformatics Section, Information Technology & Bioinformatics Program, Division of Intramural Research (DIR), (NINDS/NIH), Bethesda, MD, USA
| | - Dragan Maric
- Flow Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NINDS/NIH), Bethesda, MD, USA
| | - Giulio Volpe
- Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jennifer Kouznetsova
- National Center for Advancing Translational Sciences, National Institutes of Health (NCATS/NIH), Bethesda, MD, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health (NCATS/NIH), Bethesda, MD, USA
| | - Stefano Pluchino
- Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - John M Hallenbeck
- Stroke Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NINDS/NIH), Bethesda, MD, USA
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200
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Kuntz KW, Campbell JE, Keilhack H, Pollock RM, Knutson SK, Porter-Scott M, Richon VM, Sneeringer CJ, Wigle TJ, Allain CJ, Majer CR, Moyer MP, Copeland RA, Chesworth R. The Importance of Being Me: Magic Methyls, Methyltransferase Inhibitors, and the Discovery of Tazemetostat. J Med Chem 2016; 59:1556-64. [DOI: 10.1021/acs.jmedchem.5b01501] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Kevin W. Kuntz
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - John E. Campbell
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Heike Keilhack
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Roy M. Pollock
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Sarah K. Knutson
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Margaret Porter-Scott
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Victoria M. Richon
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Chris J. Sneeringer
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Tim J. Wigle
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Christina J. Allain
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Christina R. Majer
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Mikel P. Moyer
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Robert A. Copeland
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Richard Chesworth
- Epizyme, 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
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