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Pemovska T, Bigenzahn JW, Srndic I, Lercher A, Bergthaler A, César-Razquin A, Kartnig F, Kornauth C, Valent P, Staber PB, Superti-Furga G. Metabolic drug survey highlights cancer cell dependencies and vulnerabilities. Nat Commun 2021; 12:7190. [PMID: 34907165 PMCID: PMC8671470 DOI: 10.1038/s41467-021-27329-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Interrogation of cellular metabolism with high-throughput screening approaches can unravel contextual biology and identify cancer-specific metabolic vulnerabilities. To systematically study the consequences of distinct metabolic perturbations, we assemble a comprehensive metabolic drug library (CeMM Library of Metabolic Drugs; CLIMET) covering 243 compounds. We, next, characterize it phenotypically in a diverse panel of myeloid leukemia cell lines and primary patient cells. Analysis of the drug response profiles reveals that 77 drugs affect cell viability, with the top effective compounds targeting nucleic acid synthesis, oxidative stress, and the PI3K/mTOR pathway. Clustering of individual drug response profiles stratifies the cell lines into five functional groups, which link to specific molecular and metabolic features. Mechanistic characterization of selective responses to the PI3K inhibitor pictilisib, the fatty acid synthase inhibitor GSK2194069, and the SLC16A1 inhibitor AZD3965, bring forth biomarkers of drug response. Phenotypic screening using CLIMET represents a valuable tool to probe cellular metabolism and identify metabolic dependencies at large.
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Affiliation(s)
- Tea Pemovska
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Johannes W Bigenzahn
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Ismet Srndic
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexander Lercher
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Andreas Bergthaler
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Adrián César-Razquin
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Felix Kartnig
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Kornauth
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center Vienna, Vienna General Hospital, Medical University of Vienna, Vienna, Austria
| | - Peter Valent
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Philipp B Staber
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center Vienna, Vienna General Hospital, Medical University of Vienna, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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Neochoritis CG, Shaabani S, Ahmadianmoghaddam M, Zarganes-Tzitzikas T, Gao L, Novotná M, Mitríková T, Romero AR, Irianti MI, Xu R, Olechno J, Ellson R, Helan V, Kossenjans M, Groves MR, Dömling A. Rapid approach to complex boronic acids. Sci Adv 2019; 5:eaaw4607. [PMID: 31281893 PMCID: PMC6611686 DOI: 10.1126/sciadv.aaw4607] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/30/2019] [Indexed: 05/28/2023]
Abstract
The compatibility of free boronic acid building blocks in multicomponent reactions to readily create large libraries of diverse and complex small molecules was investigated. Traditionally, boronic acid synthesis is sequential, synthetically demanding, and time-consuming, which leads to high target synthesis times and low coverage of the boronic acid chemical space. We have performed the synthesis of large libraries of boronic acid derivatives based on multiple chemistries and building blocks using acoustic dispensing technology. The synthesis was performed on a nanomole scale with high synthesis success rates. The discovery of a protease inhibitor underscores the usefulness of the approach. Our acoustic dispensing-enabled chemistry paves the way to highly accelerated synthesis and miniaturized reaction scouting, allowing access to unprecedented boronic acid libraries.
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Affiliation(s)
- Constantinos G. Neochoritis
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Shabnam Shaabani
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Maryam Ahmadianmoghaddam
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Tryfon Zarganes-Tzitzikas
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Li Gao
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Michaela Novotná
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Tatiana Mitríková
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Atilio Reyes Romero
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Marina Ika Irianti
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Ruixue Xu
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Joe Olechno
- Labcyte Inc., 170 Rose Orchard Way, San Jose, CA 95134, USA
| | - Richard Ellson
- Labcyte Inc., 170 Rose Orchard Way, San Jose, CA 95134, USA
| | - Victoria Helan
- Hit Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Gothenburg SE-43183, Sweden
| | - Michael Kossenjans
- Hit Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Gothenburg SE-43183, Sweden
| | - Matthew R. Groves
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
| | - Alexander Dömling
- Pharmacy Department, Drug Design group, University of Groningen, Deusinglaan 1, 9700 AV Groningen, Netherlands
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Jain S, Grandits M, Richter L, Ecker GF. Structure based classification for bile salt export pump (BSEP) inhibitors using comparative structural modeling of human BSEP. J Comput Aided Mol Des 2017; 31:507-521. [PMID: 28527154 PMCID: PMC5487762 DOI: 10.1007/s10822-017-0021-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 04/30/2017] [Indexed: 01/13/2023]
Abstract
The bile salt export pump (BSEP) actively transports conjugated monovalent bile acids from the hepatocytes into the bile. This facilitates the formation of micelles and promotes digestion and absorption of dietary fat. Inhibition of BSEP leads to decreased bile flow and accumulation of cytotoxic bile salts in the liver. A number of compounds have been identified to interact with BSEP, which results in drug-induced cholestasis or liver injury. Therefore, in silico approaches for flagging compounds as potential BSEP inhibitors would be of high value in the early stage of the drug discovery pipeline. Up to now, due to the lack of a high-resolution X-ray structure of BSEP, in silico based identification of BSEP inhibitors focused on ligand-based approaches. In this study, we provide a homology model for BSEP, developed using the corrected mouse P-glycoprotein structure (PDB ID: 4M1M). Subsequently, the model was used for docking-based classification of a set of 1212 compounds (405 BSEP inhibitors, 807 non-inhibitors). Using the scoring function ChemScore, a prediction accuracy of 81% on the training set and 73% on two external test sets could be obtained. In addition, the applicability domain of the models was assessed based on Euclidean distance. Further, analysis of the protein-ligand interaction fingerprints revealed certain functional group-amino acid residue interactions that could play a key role for ligand binding. Though ligand-based models, due to their high speed and accuracy, remain the method of choice for classification of BSEP inhibitors, structure-assisted docking models demonstrate reasonably good prediction accuracies while additionally providing information about putative protein-ligand interactions.
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Affiliation(s)
- Sankalp Jain
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Melanie Grandits
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Lars Richter
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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Hsieh JH, Huang R, Lin JA, Sedykh A, Zhao J, Tice RR, Paules RS, Xia M, Auerbach SS. Real-time cell toxicity profiling of Tox21 10K compounds reveals cytotoxicity dependent toxicity pathway linkage. PLoS One 2017; 12:e0177902. [PMID: 28531190 PMCID: PMC5439695 DOI: 10.1371/journal.pone.0177902] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/04/2017] [Indexed: 01/01/2023] Open
Abstract
Cytotoxicity is a commonly used in vitro endpoint for evaluating chemical toxicity. In support of the U.S. Tox21 screening program, the cytotoxicity of ~10K chemicals was interrogated at 0, 8, 16, 24, 32, & 40 hours of exposure in a concentration dependent fashion in two cell lines (HEK293, HepG2) using two multiplexed, real-time assay technologies. One technology measures the metabolic activity of cells (i.e., cell viability, glo) while the other evaluates cell membrane integrity (i.e., cell death, flor). Using glo technology, more actives and greater temporal variations were seen in HEK293 cells, while results for the flor technology were more similar across the two cell types. Chemicals were grouped into classes based on their cytotoxicity kinetics profiles and these classes were evaluated for their associations with activity in the Tox21 nuclear receptor and stress response pathway assays. Some pathways, such as the activation of H2AX, were associated with the fast-responding cytotoxicity classes, while others, such as activation of TP53, were associated with the slow-responding cytotoxicity classes. By clustering pathways based on their degree of association to the different cytotoxicity kinetics labels, we identified clusters of pathways where active chemicals presented similar kinetics of cytotoxicity. Such linkages could be due to shared underlying biological processes between pathways, for example, activation of H2AX and heat shock factor. Others involving nuclear receptor activity are likely due to shared chemical structures rather than pathway level interactions. Based on the linkage between androgen receptor antagonism and Nrf2 activity, we surmise that a subclass of androgen receptor antagonists cause cytotoxicity via oxidative stress that is associated with Nrf2 activation. In summary, the real-time cytotoxicity screen provides informative chemical cytotoxicity kinetics data related to their cytotoxicity mechanisms, and with our analysis, it is possible to formulate mechanism-based hypotheses on the cytotoxic properties of the tested chemicals.
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Affiliation(s)
- Jui-Hua Hsieh
- Kelly Government Solutions, Durham, North Carolina, United States of America
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Ja-An Lin
- US Food and Drug Administration, Silver Spring, Maryland, United States of America
| | | | - Jinghua Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Raymond R. Tice
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Richard S. Paules
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Scott S. Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
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Kleinstreuer NC, Judson RS, Reif DM, Sipes NS, Singh AV, Chandler KJ, Dewoskin R, Dix DJ, Kavlock RJ, Knudsen TB. Environmental impact on vascular development predicted by high-throughput screening. Environ Health Perspect 2011; 119:1596-603. [PMID: 21788198 PMCID: PMC3226499 DOI: 10.1289/ehp.1103412] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 07/25/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND Understanding health risks to embryonic development from exposure to environmental chemicals is a significant challenge given the diverse chemical landscape and paucity of data for most of these compounds. High-throughput screening (HTS) in the U.S. Environmental Protection Agency (EPA) ToxCast™ project provides vast data on an expanding chemical library currently consisting of > 1,000 unique compounds across > 500 in vitro assays in phase I (complete) and Phase II (under way). This public data set can be used to evaluate concentration-dependent effects on many diverse biological targets and build predictive models of prototypical toxicity pathways that can aid decision making for assessments of human developmental health and disease. OBJECTIVE We mined the ToxCast phase I data set to identify signatures for potential chemical disruption of blood vessel formation and remodeling. METHODS ToxCast phase I screened 309 chemicals using 467 HTS assays across nine assay technology platforms. The assays measured direct interactions between chemicals and molecular targets (receptors, enzymes), as well as downstream effects on reporter gene activity or cellular consequences. We ranked the chemicals according to individual vascular bioactivity score and visualized the ranking using ToxPi (Toxicological Priority Index) profiles. RESULTS Targets in inflammatory chemokine signaling, the vascular endothelial growth factor pathway, and the plasminogen-activating system were strongly perturbed by some chemicals, and we found positive correlations with developmental effects from the U.S. EPA ToxRefDB (Toxicological Reference Database) in vivo database containing prenatal rat and rabbit guideline studies. We observed distinctly different correlative patterns for chemicals with effects in rabbits versus rats, despite derivation of in vitro signatures based on human cells and cell-free biochemical targets, implying conservation but potentially differential contributions of developmental pathways among species. Follow-up analysis with antiangiogenic thalidomide analogs and additional in vitro vascular targets showed in vitro activity consistent with the most active environmental chemicals tested here. CONCLUSIONS We predicted that blood vessel development is a target for environmental chemicals acting as putative vascular disruptor compounds (pVDCs) and identified potential species differences in sensitive vascular developmental pathways.
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Affiliation(s)
- Nicole C Kleinstreuer
- National Center for Computational Toxiciology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA.
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Drakakaki G, Robert S, Szatmari AM, Brown MQ, Nagawa S, Van Damme D, Leonard M, Yang Z, Girke T, Schmid SL, Russinova E, Friml J, Raikhel NV, Hicks GR. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. Proc Natl Acad Sci U S A 2011; 108:17850-5. [PMID: 22006339 PMCID: PMC3203817 DOI: 10.1073/pnas.1108581108] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Endomembrane trafficking relies on the coordination of a highly complex, dynamic network of intracellular vesicles. Understanding the network will require a dissection of cargo and vesicle dynamics at the cellular level in vivo. This is also a key to establishing a link between vesicular networks and their functional roles in development. We used a high-content intracellular screen to discover small molecules targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis thaliana. Tens of thousands of molecules were prescreened and a selected subset was interrogated against a panel of plasma membrane (PM) and other endomembrane compartment markers to identify molecules that altered vesicle trafficking. The extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment time matrix and revealed groups of molecules that induced similar subcellular fingerprints (clusters). This matrix provides a platform for a systems view of trafficking. Molecules from distinct clusters presented avenues and enabled an entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation. Bioactivity in human cells indicated the value of the approach to identifying small molecules that are active in diverse organisms for biology and drug discovery.
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Affiliation(s)
- Georgia Drakakaki
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Stéphanie Robert
- Department of Plant Systems Biology, University of Ghent, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, University of Ghent, 9052 Ghent, Belgium; and
| | - Anna-Maria Szatmari
- Department of Plant Systems Biology, University of Ghent, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, University of Ghent, 9052 Ghent, Belgium; and
| | - Michelle Q. Brown
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Shingo Nagawa
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Daniel Van Damme
- Department of Plant Systems Biology, University of Ghent, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, University of Ghent, 9052 Ghent, Belgium; and
| | - Marilyn Leonard
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Zhenbiao Yang
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Thomas Girke
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Sandra L. Schmid
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Eugenia Russinova
- Department of Plant Systems Biology, University of Ghent, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, University of Ghent, 9052 Ghent, Belgium; and
| | - Jiří Friml
- Department of Plant Systems Biology, University of Ghent, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, University of Ghent, 9052 Ghent, Belgium; and
| | - Natasha V. Raikhel
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Glenn R. Hicks
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
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