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Hasegawa H. Temperature-dependent intracellular crystallization of firefly luciferase in mammalian cells is suppressed by D-luciferin and stabilizing inhibitors. Exp Cell Res 2024; 440:114131. [PMID: 38876374 DOI: 10.1016/j.yexcr.2024.114131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Abstract
Firefly luciferase (Fluc) from Photinus pyralis is one of the most widely used reporter proteins in biomedical research. Despite its widespread use, Fluc's protein phase transition behaviors and phase separation characteristics have not received much attention. Current research uncovers Fluc's intrinsic property to phase separate in mammalian cells upon a simple cell culture temperature change. Specifically, Fluc spontaneously produced needle-shaped crystal-like inclusion bodies upon temperature shift to the hypothermic temperatures ranging from 25 °C to 31 °C. The crystal-like inclusion bodies were not associated with or surrounded by membranous organelles and were likely built from the cytosolic pool of Fluc. Furthermore, the crystal-like inclusion formation was suppressed when cells were cultured in the presence of D-luciferin and its synthetic analog, as well as the benzothiazole family of so-called stabilizing inhibitors. These two classes of compounds inhibited intracellular Fluc crystallization by different modes of action as they had contrasting effects on steady-state luciferase protein accumulation levels. This study suggests that, under substrate insufficient conditions, the excess Fluc phase separates into a crystal-like state that can modulate intracellular soluble enzyme availability and protein turnover rate.
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Affiliation(s)
- Haruki Hasegawa
- Discovery Protein Science, Department of Large Molecule Discovery and Research Data Science Amgen Inc., South San Francisco, CA 94080, USA.
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2
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Roennfeldt AE, Allen TP, Trowbridge BN, Beard MR, Whitelaw ML, Russell DL, Bersten DC, Peet DJ. NanoFIRE: A NanoLuciferase and Fluorescent Integrated Reporter Element for Robust and Sensitive Investigation of HIF and Other Signalling Pathways. Biomolecules 2023; 13:1545. [PMID: 37892227 PMCID: PMC10605489 DOI: 10.3390/biom13101545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The Hypoxia Inducible Factor (HIF) transcription factors are imperative for cell adaption to low oxygen conditions and development; however, they also contribute to ischaemic disease and cancer. To identify novel genetic regulators which target the HIF pathway or small molecules for therapeutic use, cell-based reporter systems are commonly used. Here, we present a new, highly sensitive and versatile reporter system, NanoFIRE: a NanoLuciferase and Fluorescent Integrated Reporter Element. Under the control of a Hypoxic Response Element (HRE-NanoFIRE), this system is a robust sensor of HIF activity within cells and potently responds to both hypoxia and chemical inducers of the HIF pathway in a highly reproducible and sensitive manner, consistently achieving 20 to 150-fold induction across different cell types and a Z' score > 0.5. We demonstrate that the NanoFIRE system is adaptable via substitution of the response element controlling NanoLuciferase and show that it can report on the activity of the transcriptional regulator Factor Inhibiting HIF, and an unrelated transcription factor, the Progesterone Receptor. Furthermore, the lentivirus-mediated stable integration of NanoFIRE highlights the versatility of this system across a wide range of cell types, including primary cells. Together, these findings demonstrate that NanoFIRE is a robust reporter system for the investigation of HIF and other transcription factor-mediated signalling pathways in cells, with applications in high throughput screening for the identification of novel small molecule and genetic regulators.
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Affiliation(s)
- Alison E. Roennfeldt
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, SA 5006, Australia;
| | - Timothy P. Allen
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
| | - Brooke N. Trowbridge
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Michael R. Beard
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Murray L. Whitelaw
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
- ASEAN Microbiome Nutrition Centre, National Neuroscience Institute, Singapore 169857, Singapore
| | - Darryl L. Russell
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, SA 5006, Australia;
| | - David C. Bersten
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, SA 5006, Australia;
| | - Daniel J. Peet
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
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3
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Ren Q, Bakker W, de Haan L, Rietjens IMCM, Bouwmeester H. Induction of Nrf2-EpRE-mediated gene expression by hydroxyanthraquinones present in extracts from traditional Chinese medicine and herbs. Food Chem Toxicol 2023; 176:113802. [PMID: 37116774 DOI: 10.1016/j.fct.2023.113802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 04/30/2023]
Abstract
Hydroxyanthraquinones that can be present in traditional Chinese medicine (TCM) and herbal extracts have claimed beneficial intestinal effects. We examined the ability of a panel hydroxyanthraquinones, and methanolic extracts from selected TCM and herbal granules to activate Nrf2-EpRE mediated gene expression using a reporter-gene assay. The results indicate that purpurin, aloe-emodin, 2-hydroxy-3-methylanthraquinone and rhein induced Nrf2 mediated gene expressions with a high induction factor (IFs>10), with BMCL10 values (the lower confidence limit of the concentration giving 10% added response above background) of 16 μM, 1.1 μM, 23 μM and 2.3 μM, respectively, while aurantio-obtusin, obtusifolin, rubiadin 1-methyl ether and emodin were less potent (IFs<5), with BMCL10 values for added response above background level of 4.6 μM, 15 μM, 9.8 μM and 3.8 μM, respectively. All TCM extracts and the herbal extracts of Aloe Vera, Polygonum multiflorum, Rubia (cordifolia) and Rheum officinale activated the Nrf2-EpRE pathway. Of the TCM extracts, Chuan-Xin-Lian-Kang-Yan-Pian was the most potent Nrf2-inducer. LC-MS/MS analysis indicated the presence of selected hydroxyanthraquinones in the extracts and herbs, in part explaining their Nrf2-EpRE mediated activity. In conclusion, different hydroxyanthraquinones have different potencies of Nrf2 activation. The Nrf2 activation by extracts from TCM and herbs can be partially explained by the presence of selected hydroxyanthraquinones.
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Affiliation(s)
- Qiuhui Ren
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands.
| | - Wouter Bakker
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Laura de Haan
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Hans Bouwmeester
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
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4
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Kumar A, Aglyamova G, Yim Y, Bailey AO, Lynch H, Powell R, Nguyen N, Rosenthal Z, Zhao WN, Li Y, Chen J, Fan S, Lee H, Russell W, Stephan C, Robison A, Haggarty S, Nestler E, Zhou J, Machius M, Rudenko G. Chemically targeting the redox switch in AP1 transcription factor ΔFOSB. Nucleic Acids Res 2022; 50:9548-9567. [PMID: 36039764 PMCID: PMC9458432 DOI: 10.1093/nar/gkac710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 12/24/2022] Open
Abstract
The AP1 transcription factor ΔFOSB, a splice variant of FOSB, accumulates in the brain in response to chronic insults such as exposure to drugs of abuse, depression, Alzheimer's disease and tardive dyskinesias, and mediates subsequent long-term neuroadaptations. ΔFOSB forms heterodimers with other AP1 transcription factors, e.g. JUND, that bind DNA under control of a putative cysteine-based redox switch. Here, we reveal the structural basis of the redox switch by determining a key missing crystal structure in a trio, the ΔFOSB/JUND bZIP domains in the reduced, DNA-free form. Screening a cysteine-focused library containing 3200 thiol-reactive compounds, we identify specific compounds that target the redox switch, validate their activity biochemically and in cell-based assays, and show that they are well tolerated in different cell lines despite their general potential to bind to cysteines covalently. A crystal structure of the ΔFOSB/JUND bZIP domains in complex with a redox-switch-targeting compound reveals a deep compound-binding pocket near the DNA-binding site. We demonstrate that ΔFOSB, and potentially other, related AP1 transcription factors, can be targeted specifically and discriminately by exploiting unique structural features such as the redox switch and the binding partner to modulate biological function despite these proteins previously being thought to be undruggable.
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Affiliation(s)
| | | | - Yun Young Yim
- Nash Family Department of Neuroscience and the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Haley M Lynch
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Reid T Powell
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Nghi D Nguyen
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Zachary Rosenthal
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Wen-Ning Zhao
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Yi Li
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jianping Chen
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Shanghua Fan
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Hubert Lee
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Clifford Stephan
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Alfred J Robison
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Eric J Nestler
- Nash Family Department of Neuroscience and the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mischa Machius
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Gabby Rudenko
- To whom correspondence should be addressed. Tel: +1 409 772 6292; Fax: +1 409 772 9642;
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5
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Anywar GU, Kakudidi E, Oryem-Origa H, Schubert A, Jassoy C. Cytotoxicity of Medicinal Plant Species Used by Traditional Healers in Treating People Suffering From HIV/AIDS in Uganda. FRONTIERS IN TOXICOLOGY 2022; 4:832780. [PMID: 35586188 PMCID: PMC9108544 DOI: 10.3389/ftox.2022.832780] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction: Many people living with HIV/AIDS (PLHIV) in Uganda widely use herbal medicines. However, their toxicity and safety have not been investigated. The use of these plants can potentially cause harmful effects to the health of patients. The purpose of this study was to determine the cytotoxicity of some commonly used medicinal plant species used by PLHIV. Methods: The cytotoxicity of the plant extracts was determined with the AlamarBlue cell viability assay using the human glioblastoma cell line U87.CD4.CXCR4. The cells were treated with varying concentrations of extracts of Warburgia ugandensis, Erythrina abyssinica, Cryptolepis sanguinolenta, Albizia coriaria, Psorospermum febrifugium, Gymnosporia senegalensis, Zanthoxylum chalybeum, Securidaca longipendunculata, Vachellia hockii, Gardenia ternifolia, and Bridelia micrantha reconstituted with ethanol and dimethyl sulfoxide (DMSO). Using regression analysis, the half maximal cytotoxic concentration (CC50) of the plant extracts were calculated from exponential curve fits, since they provided the highest coefficient of determination, R2. Results: The ethanol extracts of W. ugandensis (CC50 = 7.6 μg/ml) and A. coriaria (CC50 = 1.5 μg/ml) as well as the DMSO-reconstituted extracts of W. ugandensis (CC50 = 6.4 μg/ml) and A. coriria (CC50 = < 4 μg/ml) were highly cytotoxic. The cytotoxicity of W. ugandensis and A. coriaria compared well with the indigenous traditional knowledge of the toxic effects experienced when the plants were not used correctly. However, the cytotoxicity of most of the plant extracts (15/22) was low to moderate (CC50 = 21–200 μg/ml). Conclusion: Most of the plant species tested in this study had low to moderate cytotoxicity against U87.CD4.CXCR4 cells, except W. ugandensis and A. coriria which were highly cytotoxic.
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Affiliation(s)
- Godwin Upoki Anywar
- Department of Plant Sciences, Microbiology & Biotechnology, College of Natural Sciences, Makerere University, Kampala, Uganda
- Fraunhofer Institute for Cell Therapy & Immunology (IZI), Leipzig, Germany
- Institute for Medical Microbiology & Virology, University Clinics & Faculty of Medicine, University of Leipzig, Leipzig, Germany
- *Correspondence: Godwin Upoki Anywar, , ,
| | - Esezah Kakudidi
- Department of Plant Sciences, Microbiology & Biotechnology, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Hannington Oryem-Origa
- Department of Plant Sciences, Microbiology & Biotechnology, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Andreas Schubert
- Fraunhofer Institute for Cell Therapy & Immunology (IZI), Leipzig, Germany
| | - Christian Jassoy
- Institute for Medical Microbiology & Virology, University Clinics & Faculty of Medicine, University of Leipzig, Leipzig, Germany
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Cykowiak M, Kleszcz R, Kucińska M, Paluszczak J, Szaefer H, Plewiński A, Piotrowska-Kempisty H, Murias M, Krajka-Kuźniak V. Attenuation of Pancreatic Cancer In Vitro and In Vivo via Modulation of Nrf2 and NF-κB Signaling Pathways by Natural Compounds. Cells 2021; 10:3556. [PMID: 34944062 PMCID: PMC8700195 DOI: 10.3390/cells10123556] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/04/2021] [Accepted: 12/14/2021] [Indexed: 12/16/2022] Open
Abstract
Pancreatic cancer is a disease in which deregulation of signaling pathways plays a key role, thus searching for their novel modulators is a promising therapeutic strategy. Hence, in this study, the effect of phytochemical combinations on the canonical and non-canonical activation of Nrf2 and its interaction with the NF-κB pathway was evaluated in extensively proliferating pancreatic cancer cell line, PSN-1, in comparison to non-cancerous MS1 cells. The activation of Nrf2 and NF-κB, expression of their target genes, and effect on cell survival were assessed in PSN-1 cells. The tumor burden was evaluated in mice carrying xenografts. PSN-1 cells were more sensitive to the tested compounds as compared to the MS1 cell line. Combination of xanthohumol and phenethyl isothiocyanate was more effective than single compounds at decreasing the canonical and non-canonical activation of Nrf2 in PSN-1 cancer cells. Decreased activation of NF-κB, and subsequent reduced cytosolic COX-2 and nuclear STAT3 level indicated their anti-inflammatory and pro-apoptotic activities. In vivo studies showed the partial response in groups treated with xanthohumol or the combination of xanthohumol and phenethyl isothiocyanate. Overall, these results suggest that the combination of xanthohumol and phenethyl isothiocyanate may be a promising therapeutic candidate against pancreatic cancer.
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Affiliation(s)
- Marta Cykowiak
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, 4, Święcickiego Street, 60-781 Poznań, Poland; (M.C.); (R.K.); (J.P.); (H.S.)
| | - Robert Kleszcz
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, 4, Święcickiego Street, 60-781 Poznań, Poland; (M.C.); (R.K.); (J.P.); (H.S.)
| | - Małgorzata Kucińska
- Department of Toxicology, Poznan University of Medical Sciences, 30, Dojazd Street, 60-631 Poznań, Poland; (M.K.); (H.P.-K.); (M.M.)
| | - Jarosław Paluszczak
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, 4, Święcickiego Street, 60-781 Poznań, Poland; (M.C.); (R.K.); (J.P.); (H.S.)
| | - Hanna Szaefer
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, 4, Święcickiego Street, 60-781 Poznań, Poland; (M.C.); (R.K.); (J.P.); (H.S.)
| | - Adam Plewiński
- Centre for Advanced Technologies, Adam Mickiewicz University, 10, Uniwersytetu Poznańskiego Street, 61-614 Poznań, Poland;
| | - Hanna Piotrowska-Kempisty
- Department of Toxicology, Poznan University of Medical Sciences, 30, Dojazd Street, 60-631 Poznań, Poland; (M.K.); (H.P.-K.); (M.M.)
| | - Marek Murias
- Department of Toxicology, Poznan University of Medical Sciences, 30, Dojazd Street, 60-631 Poznań, Poland; (M.K.); (H.P.-K.); (M.M.)
| | - Violetta Krajka-Kuźniak
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, 4, Święcickiego Street, 60-781 Poznań, Poland; (M.C.); (R.K.); (J.P.); (H.S.)
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7
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Stahl F, Denner P, Piston D, Evert BO, de Boni L, Schmitt I, Breuer P, Wüllner U. Activators of alpha synuclein expression identified by reporter cell line-based high throughput drug screen. Sci Rep 2021; 11:19857. [PMID: 34615900 PMCID: PMC8494889 DOI: 10.1038/s41598-021-98841-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/08/2021] [Indexed: 11/29/2022] Open
Abstract
Multiplications, mutations and dysregulation of the alpha synuclein gene (SNCA) are associated with the demise of dopaminergic neurons and are considered to play important roles in the pathogenesis of familial and sporadic forms of Parkinson's disease. Regulation of SNCA expression might thus be an appropriate target for treatment. We aimed to identify specific modulators of SNCA transcription, generated CRISPR/Cas9 modified SNCA-GFP-luciferase (LUC) genomic fusion- and control cell lines and screened a library of 1649 bioactive compounds, including the FDA approved drugs. We found no inhibitors but three selective activators which increased SNCA mRNA and protein levels.
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Affiliation(s)
- Fabian Stahl
- DZNE, German Center for Neurodegenerative Diseases, Venusberg-Campus 1/99, 53127, Bonn, Germany
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
| | - Philip Denner
- DZNE, German Center for Neurodegenerative Diseases, Venusberg-Campus 1/99, 53127, Bonn, Germany
| | - Dominik Piston
- DZNE, German Center for Neurodegenerative Diseases, Venusberg-Campus 1/99, 53127, Bonn, Germany
| | - Bernd O Evert
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
| | - Laura de Boni
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
| | - Ina Schmitt
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
| | - Peter Breuer
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany.
| | - Ullrich Wüllner
- DZNE, German Center for Neurodegenerative Diseases, Venusberg-Campus 1/99, 53127, Bonn, Germany.
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany.
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8
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Martinez NJ, Braisted JC, Dranchak PK, Moran JJ, Larson H, Queme B, Pak E, Dutra A, Rai G, Cheng KCC, Svaren J, Inglese J. Genome-Edited Coincidence and PMP22-HiBiT Fusion Reporter Cell Lines Enable an Artifact-Suppressive Quantitative High-Throughput Screening Strategy for PMP22 Gene-Dosage Disorder Drug Discovery. ACS Pharmacol Transl Sci 2021; 4:1422-1436. [PMID: 34423274 DOI: 10.1021/acsptsci.1c00110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Indexed: 12/23/2022]
Abstract
Charcot-Marie-Tooth 1A (CMT1A) is the most common form of hereditary peripheral neuropathies, characterized by genetic duplication of the critical myelin gene Peripheral Myelin Protein 22 (PMP22). PMP22 overexpression results in abnormal Schwann cell differentiation, leading to axonal loss and muscle wasting. Since regulation of PMP22 expression is a major target of therapeutic discovery for CMT1A, we sought to establish unbiased approaches that allow the identification of therapeutic agents for this disease. Using genome editing, we generated a coincidence reporter assay that accurately monitors Pmp22 transcript levels in the S16 rat Schwann cell line, while reducing reporter-based false positives. A quantitative high-throughput screen (qHTS) of 42 577 compounds using this assay revealed diverse novel chemical classes that reduce endogenous Pmp22 transcript levels. Moreover, some of these classes show pharmacological specificity in reducing Pmp22 over another major myelin-associated gene, Mpz (Myelin protein zero). Finally, to investigate whether compound-mediated reduction of Pmp22 transcripts translates to reduced PMP22 protein levels, we edited the S16 genome to generate a reporter assay that expresses a PMP22-HiBiT fusion protein using CRISPR/Cas9. Overall, we present a screening platform that combines genome edited cell lines encoding reporters that monitor transcriptional and post-translational regulation of PMP22 with titration-based screening (e.g., qHTS), which could be efficiently incorporated into drug discovery campaigns for CMT1A.
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Affiliation(s)
- Natalia J Martinez
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - John C Braisted
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Patricia K Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - John J Moran
- Department of Comparative Biosciences, and Waisman Center, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Hunter Larson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Bryan Queme
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Evgenia Pak
- National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland 20817, United States
| | - Amalia Dutra
- National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland 20817, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Ken Chih-Chien Cheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - John Svaren
- Department of Comparative Biosciences, and Waisman Center, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States.,National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland 20817, United States
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9
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Evaluation of Firefly and Renilla Luciferase Inhibition in Reporter-Gene Assays: A Case of Isoflavonoids. Int J Mol Sci 2021; 22:ijms22136927. [PMID: 34203212 PMCID: PMC8268740 DOI: 10.3390/ijms22136927] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/21/2022] Open
Abstract
Firefly luciferase is susceptible to inhibition and stabilization by compounds under investigation for biological activity and toxicity. This can lead to false-positive results in in vitro cell-based assays. However, firefly luciferase remains one of the most commonly used reporter genes. Here, we evaluated isoflavonoids for inhibition of firefly luciferase. These natural compounds are often studied using luciferase reporter-gene assays. We used a quantitative structure–activity relationship (QSAR) model to compare the results of in silico predictions with a newly developed in vitro assay that enables concomitant detection of inhibition of firefly and Renilla luciferases. The QSAR model predicted a moderate to high likelihood of firefly luciferase inhibition for all of the 11 isoflavonoids investigated, and the in vitro assays confirmed this for seven of them: daidzein, genistein, glycitein, prunetin, biochanin A, calycosin, and formononetin. In contrast, none of the 11 isoflavonoids inhibited Renilla luciferase. Molecular docking calculations indicated that isoflavonoids interact favorably with the D-luciferin binding pocket of firefly luciferase. These data demonstrate the importance of reporter-enzyme inhibition when studying the effects of such compounds and suggest that this in vitro assay can be used to exclude false-positives due to firefly or Renilla luciferase inhibition, and to thus define the most appropriate reporter gene.
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10
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Compounds with multitarget activity: structure-based analysis and machine learning. FUTURE DRUG DISCOVERY 2020. [DOI: 10.4155/fdd-2020-0014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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11
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12
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Lungu-Mitea S, Lundqvist J. Potentials and pitfalls of transient in vitro reporter bioassays: interference by vector geometry and cytotoxicity in recombinant zebrafish cell lines. Arch Toxicol 2020; 94:2769-2784. [PMID: 32447522 PMCID: PMC7395025 DOI: 10.1007/s00204-020-02783-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/07/2020] [Indexed: 12/03/2022]
Abstract
The water framework directive re-evaluation proposes the integration of effect-based tools, increasing the need for alternative methods. Especially within aquatic toxicology, coverage of specific toxicity pathways is scarce, and most applications are based on mammalian or bacterial models, not reflecting realistic exposure scenarios. The use of transient reporter gene assays in cells from organisms of interest could be a quick and inexpensive solution. However, interference with cellular homeostasis may impact the system beyond the function of the manipulated gene and thus lead to non-specific results. We describe how varying vector geometry and different regulatory gene elements on plasmids used for transfection in zebrafish hepatocytes and embryonic fibroblasts may lead up to a tenfold difference in potency. Cells were transiently co-transfected with an Nrf2-responsive Firefly luciferase reporter plasmid and eight different Renilla luciferase normalization plasmids. Transfected cells were exposed to two different regimes (0.1–100 µM and 7.8–250 µM) of the oxidative stress-inducing compounds, sulforaphane, tertbutylhydroquinone, and metazachlor. Nrf2 activity was measured in dual-luciferase assays. In parallel, cytotoxicity was assessed for different endpoints (energy metabolism, protein amount, membrane stability, and cell proliferation) in non-transfected cells and cells co-transfected with constructs of increasing size, to be used for normalization. Transfected cells were more susceptible to cytotoxicity in a vector size-dependent manner. Conclusively, we report that vector geometries (size, backbones, gene-regulatory units), cell line (tissue origin), applied transfection methods, and signal normalization may alter the sensitivity of reporter bioassays in a synergistic manner. Further, we propose that thorough bioassay design is needed to ensure reliability and regulatory acceptance.
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Affiliation(s)
- Sebastian Lungu-Mitea
- Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, SE-750 07, Uppsala, Sweden.
| | - Johan Lundqvist
- Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, SE-750 07, Uppsala, Sweden
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13
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Kenda M, Sollner Dolenc M. Computational Study of Drugs Targeting Nuclear Receptors. Molecules 2020; 25:E1616. [PMID: 32244747 PMCID: PMC7180905 DOI: 10.3390/molecules25071616] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 03/28/2020] [Accepted: 03/31/2020] [Indexed: 12/18/2022] Open
Abstract
Endocrine-disrupting chemicals have been shown to interfere with the endocrine system function at the level of hormone synthesis, transport, metabolism, binding, action, and elimination. They are associated with several health problems in humans: obesity, diabetes mellitus, infertility, impaired thyroid and neuroendocrine functions, neurodevelopmental problems, and cancer are among them. As drugs are chemicals humans can be frequently exposed to for longer periods of time, special emphasis should be put on their endocrine-disrupting potential. In this study, we conducted a screen of 1046 US-approved and marketed small-molecule drugs (molecular weight between 60 and 600) for estimating their endocrine-disrupting properties. Binding affinity to 12 nuclear receptors was assessed with a molecular-docking program, Endocrine Disruptome. We identified 130 drugs with a high binding affinity to a nuclear receptor that is not their pharmacological target. In a subset of drugs with predicted high binding affinities to a nuclear receptor with Endocrine Disruptome, the positive predictive value was 0.66 when evaluated with in silico results obtained with another molecular docking program, VirtualToxLab, and 0.32 when evaluated with in vitro results from the Tox21 database. Computational screening was proven useful in prioritizing drugs for in vitro testing. We suggest that the novel interactions of drugs with nuclear receptors predicted here are further investigated.
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Affiliation(s)
| | - Marija Sollner Dolenc
- Faculty of Pharmacy; University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia;
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14
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Kaschubek T, Mayer E, Rzesnik S, Grenier B, Bachinger D, Schieder C, König J, Teichmann K. Effects of phytogenic feed additives on cellular oxidative stress and inflammatory reactions in intestinal porcine epithelial cells1. J Anim Sci 2020; 96:3657-3669. [PMID: 29982751 PMCID: PMC6127757 DOI: 10.1093/jas/sky263] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/05/2018] [Indexed: 11/14/2022] Open
Abstract
Due to increasing concerns about the use of antibiotic growth promoters (AGP) in livestock production and their complete ban in the European Union in 2006, suitable alternatives are urgently needed. Among others, anti-inflammatory activities of AGP are discussed as their putative mode of action. As numerous phytochemicals are known to modulate the cellular antioxidant capacity and immune response, we studied the antioxidative and anti-inflammatory properties of a phytogenic (plant-derived) feed additive (PFA) in intestinal porcine epithelial cells (IPEC-J2). The effects of the PFA were compared with those of selected phytogenic ingredients (grape seed extract [GRS], licorice extract [LIC], menthol [MENT], methyl salicylate [MES], oak bark extract [OAK], oregano essential oil [ORE], and a plant powder mix [PLA]), and with the effects of the AGP tylosin (TYL). Oxidative or inflammatory stress was induced by stimulating IPEC-J2 with hydrogen peroxide (H2O2; 0.5 mM) or tumor necrosis factor alpha (TNF-α; 10 ng/mL), respectively. The antioxidative effects of feed additives were assessed with a reactive oxygen species (ROS)-sensitive probe and by measuring the expression of 6 antioxidative target genes via quantitative real-time PCR (RT-qPCR). Anti-inflammatory potential was analyzed using a nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) reporter gene assay. Moreover, the expression levels of 6 NF-κB target genes were measured using RT-qPCR analysis, and the release of IL-6 was analyzed via ELISA. Significant decreases in cellular ROS upon H2O2 treatment were observed for the PFA (P < 0.001), LIC (P < 0.001), ORE (P < 0.05), and GRS (P < 0.01). No significant changes in the expression of antioxidative genes were found. NF-κB activation upon TNF-α treatment was significantly inhibited by the PFA (P < 0.05) and by ORE (P < 0.001). Moreover, the PFA and ORE significantly reduced the gene expression of IL-6 (P < 0.001), IL-8 (P < 0.001), and C-C motif chemokine ligand 2 (CCL2; P < 0.05), as well as the release of IL-6 (P < 0.05). The other phytogenic compounds as well as the AGP TYL did not significantly affect any of the inflammatory parameters. In summary, we revealed the antioxidative properties of the PFA, LIC, ORE, and GRS, as well as anti-inflammatory properties of the PFA and ORE in IPEC-J2, providing a better understanding of the mode of action of this PFA under our experimental conditions.
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Affiliation(s)
- Theresa Kaschubek
- BIOMIN Research Center, Tulln an der Donau, Austria.,Department of Nutritional Science, University of Vienna, Vienna, Austria
| | | | | | | | | | | | - Jürgen König
- Department of Nutritional Science, University of Vienna, Vienna, Austria
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15
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Yang ZY, Dong J, Yang ZJ, Lu AP, Hou TJ, Cao DS. Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays. J Chem Inf Model 2020; 60:2031-2043. [PMID: 32202787 DOI: 10.1021/acs.jcim.9b01188] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Luciferase-based bioluminescence detection techniques are highly favored in high-throughput screening (HTS), in which the firefly luciferase (FLuc) is the most commonly used variant. However, FLuc inhibitors can interfere with the activity of luciferase, which may result in false positive signals in HTS assays. In order to reduce the unnecessary cost of time and money, an in silico prediction model for FLuc inhibitors is highly desirable. In this study, we built an extensive data set consisting of 20 888 FLuc inhibitors and 198 608 noninhibitors, and then developed a group of classification models based on the combination of three machine learning (ML) algorithms and four types of molecular representations. The best prediction model based on XGBoost and ECFP4 and MOE2d descriptors yielded a balanced accuracy (BA) of 0.878 and an area under the receiver operating characteristic curve (AUC) value of 0.958 for the validation set, and a BA of 0.886 and an AUC of 0.947 for the test set. Three external validation sets, including set 1 (3231 FLuc inhibitors and 69 783 noninhibitors), set 2 (695 FLuc inhibitors and 75 913 noninhibitors), and set 3 (1138 FLuc inhibitors and 8155 noninhibitors), were used to verify the predictive ability of our models. The BA values for the three external validation sets given by the best model are 0.864, 0.845, and 0.791, respectively. In addition, the important features or structural fragments related to FLuc inhibitors were recognized by the Shapley additive explanations (SHAP) method along with their influences on predictions, which may provide valuable clues to detecting undesirable luciferase inhibitors. Based on the important and explanatory features, 16 rules were proposed for detecting FLuc inhibitors, which can achieve a correction rate of 70% for FLuc inhibitors. Furthermore, a comparison with existing prediction rules and models for FLuc inhibitors used in virtual screening verified the high reliability of the models and rules proposed in this study. We also used the model to screen three curated chemical databases, and almost 10% of the molecules in the evaluated databases were predicted as inhibitors, highlighting the potential risk of false positives in luciferase-based assays. Finally, a public web server called ChemFLuc was developed (http://admet.scbdd.com/chemfluc/index/), and it offers a free available service to predict potential FLuc inhibitors.
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Affiliation(s)
- Zi-Yi Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410003, P.R. China
| | - Jie Dong
- Central South University of Forestry and Technology, Changsha, 410004, P.R. China
| | - Zhi-Jiang Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410003, P.R. China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, P.R. China
| | - Ting-Jun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P.R. China
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410003, P.R. China.,Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, P.R. China
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16
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Babbs A, Berg A, Chatzopoulou M, Davies KE, Davies SG, Edwards B, Elsey DJ, Emer E, Figuccia AL, Fletcher AM, Guiraud S, Harriman S, Moir L, Robinson N, Rowley JA, Russell AJ, Squire SE, Thomson JE, Tinsley JM, Wilson FX, Wynne GM. Synthesis of SMT022357 enantiomers and in vivo evaluation in a Duchenne muscular dystrophy mouse model. Tetrahedron 2020; 76:130819. [PMID: 32713969 PMCID: PMC7369641 DOI: 10.1016/j.tet.2019.130819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 01/02/2023]
Abstract
Following on from ezutromid, the first-in-class benzoxazole utrophin modulator that progressed to Phase 2 clinical trials for the treatment of Duchenne muscular dystrophy, a new chemotype was designed to optimise its physicochemical and ADME profile. Herein we report the synthesis of SMT022357, a second generation utrophin modulator preclinical candidate, and an asymmetric synthesis of its constituent enantiomers. The pharmacological properties of both enantiomers were evaluated in vitro and in vivo. No significant difference in the activity or efficacy was observed between the two enantiomers; activity was found to be comparable to the racemic mixture.
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Affiliation(s)
- Arran Babbs
- Department of Anatomy and Genetics, MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX1 3PT, UK
| | - Adam Berg
- Department of Anatomy and Genetics, MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX1 3PT, UK
| | - Maria Chatzopoulou
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Kay E. Davies
- Department of Anatomy and Genetics, MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX1 3PT, UK
| | - Stephen G. Davies
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Benjamin Edwards
- Department of Anatomy and Genetics, MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX1 3PT, UK
| | - David J. Elsey
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, OX14 4SB, UK
| | - Enrico Emer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Aude L.A. Figuccia
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ai M. Fletcher
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Simon Guiraud
- Department of Anatomy and Genetics, MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX1 3PT, UK
| | - Shawn Harriman
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, OX14 4SB, UK
| | - Lee Moir
- Department of Anatomy and Genetics, MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX1 3PT, UK
| | - Neil Robinson
- S.H.B. Enterprises Ltd, 55 Station Road, Beaconsfield, HP19 1QL, UK
| | - Jessica A. Rowley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Angela J. Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK
| | - Sarah E. Squire
- Department of Anatomy and Genetics, MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX1 3PT, UK
| | - James E. Thomson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Jonathon M. Tinsley
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, OX14 4SB, UK
| | - Francis X. Wilson
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, OX14 4SB, UK
| | - Graham M. Wynne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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17
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Lee OW, Austin S, Gamma M, Cheff DM, Lee TD, Wilson KM, Johnson J, Travers J, Braisted JC, Guha R, Klumpp-Thomas C, Shen M, Hall MD. Cytotoxic Profiling of Annotated and Diverse Chemical Libraries Using Quantitative High-Throughput Screening. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:9-20. [PMID: 31498718 PMCID: PMC10791069 DOI: 10.1177/2472555219873068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cell-based phenotypic screening is a commonly used approach to discover biological pathways, novel drug targets, chemical probes, and high-quality hit-to-lead molecules. Many hits identified from high-throughput screening campaigns are ruled out through a series of follow-up potency, selectivity/specificity, and cytotoxicity assays. Prioritization of molecules with little or no cytotoxicity for downstream evaluation can influence the future direction of projects, so cytotoxicity profiling of screening libraries at an early stage is essential for increasing the likelihood of candidate success. In this study, we assessed the cell-based cytotoxicity of nearly 10,000 compounds in the National Institutes of Health, National Center for Advancing Translational Sciences annotated libraries and more than 100,000 compounds in a diversity library against four normal cell lines (HEK 293, NIH 3T3, CRL-7250, and HaCat) and one cancer cell line (KB 3-1, a HeLa subline). This large-scale library profiling was analyzed for overall screening outcomes, hit rates, pan-activity, and selectivity. For the annotated library, we also examined the primary targets and mechanistic pathways regularly associated with cell death. To our knowledge, this is the first study to use high-throughput screening to profile a large screening collection (>100,000 compounds) for cytotoxicity in both normal and cancer cell lines. The results generated here constitute a valuable resource for the scientific community and provide insight into the extent of cytotoxic compounds in screening libraries, allowing for the identification and avoidance of compounds with cytotoxicity during high-throughput screening campaigns.
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Affiliation(s)
- Olivia W. Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Shelley Austin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Madison Gamma
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Dorian M. Cheff
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Tobie D. Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Kelli M. Wilson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Joseph Johnson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jameson Travers
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - John C. Braisted
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Rajarshi Guha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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18
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Wilkinson IVL, Reynolds JK, Galan SRG, Vuorinen A, Sills AJ, Pires E, Wynne GM, Wilson FX, Russell AJ. Characterisation of utrophin modulator SMT C1100 as a non-competitive inhibitor of firefly luciferase. Bioorg Chem 2019; 94:103395. [PMID: 31733898 DOI: 10.1016/j.bioorg.2019.103395] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
Firefly luciferase (FLuc) is a powerful tool for molecular and cellular biology, and popular in high-throughput screening and drug discovery. However, FLuc assays have been plagued with positive and negative artefacts due to stabilisation and inhibition by small molecules from a range of chemical classes. Here we disclose Phase II clinical compound SMT C1100 for the treatment of Duchenne muscular dystrophy as an FLuc inhibitor (KD of 0.40 ± 0.15 µM). Enzyme kinetic studies using SMT C1100 and other non-competitive inhibitors including resveratrol and NFκBAI4 identified previously undescribed modes of inhibition with respect to FLuc's luciferyl adenylate intermediate. Employing a photoaffinity strategy to identify SMT C1100's binding site, a photolabelled SMT C1100 probe instead underwent FLuc-dependent photooxidation. Our findings support novel binding sites on FLuc for non-competitive inhibitors.
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Affiliation(s)
- Isabel V L Wilkinson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Jessica K Reynolds
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Sébastien R G Galan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Aini Vuorinen
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Adam J Sills
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Elisabete Pires
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Graham M Wynne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Francis X Wilson
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, Oxfordshire OX14 4SB, UK
| | - Angela J Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3PQ, UK.
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19
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Atkinson BN, Steadman D, Zhao Y, Sipthorp J, Vecchia L, Ruza RR, Jeganathan F, Lines G, Frew S, Monaghan A, Kjær S, Bictash M, Jones EY, Fish PV. Discovery of 2-phenoxyacetamides as inhibitors of the Wnt-depalmitoleating enzyme NOTUM from an X-ray fragment screen. MEDCHEMCOMM 2019; 10:1361-1369. [PMID: 31534655 PMCID: PMC6727465 DOI: 10.1039/c9md00096h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 12/11/2022]
Abstract
NOTUM is a carboxylesterase that has been shown to act by mediating the O-depalmitoleoylation of Wnt proteins resulting in suppression of Wnt signaling. Here, we describe the development of NOTUM inhibitors that restore Wnt signaling for use in in vitro disease models where NOTUM over activity is an underlying cause. A crystallographic fragment screen with NOTUM identified 2-phenoxyacetamide 3 as binding in the palmitoleate pocket with modest inhibition activity (IC50 33 μM). Optimization of hit 3 by SAR studies guided by SBDD identified indazole 38 (IC50 0.032 μM) and isoquinoline 45 (IC50 0.085 μM) as potent inhibitors of NOTUM. The binding of 45 to NOTUM was rationalized through an X-ray co-crystal structure determination which showed a flipped binding orientation compared to 3. However, it was not possible to combine NOTUM inhibition activity with metabolic stability as the majority of the compounds tested were rapidly metabolized in an NADPH-independent manner.
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Affiliation(s)
- Benjamin N Atkinson
- Alzheimer's Research UK UCL Drug Discovery Institute , University College London , Cruciform Building, Gower Street , London , WC1E 6BT , UK . ; Tel: +44 (0)20 7679 6971
| | - David Steadman
- Alzheimer's Research UK UCL Drug Discovery Institute , University College London , Cruciform Building, Gower Street , London , WC1E 6BT , UK . ; Tel: +44 (0)20 7679 6971
| | - Yuguang Zhao
- Division of Structural Biology , Wellcome Centre for Human Genetics , University of Oxford , The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive , Oxford , OX3 7BN , UK . ; Tel: +44 (0)1865 287 546
| | - James Sipthorp
- Alzheimer's Research UK UCL Drug Discovery Institute , University College London , Cruciform Building, Gower Street , London , WC1E 6BT , UK . ; Tel: +44 (0)20 7679 6971
- The Francis Crick Institute , 1 Midland Road , London , NW1 1AT , UK
| | - Luca Vecchia
- Division of Structural Biology , Wellcome Centre for Human Genetics , University of Oxford , The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive , Oxford , OX3 7BN , UK . ; Tel: +44 (0)1865 287 546
| | - Reinis R Ruza
- Division of Structural Biology , Wellcome Centre for Human Genetics , University of Oxford , The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive , Oxford , OX3 7BN , UK . ; Tel: +44 (0)1865 287 546
| | - Fiona Jeganathan
- Alzheimer's Research UK UCL Drug Discovery Institute , University College London , Cruciform Building, Gower Street , London , WC1E 6BT , UK . ; Tel: +44 (0)20 7679 6971
| | - Georgie Lines
- Alzheimer's Research UK UCL Drug Discovery Institute , University College London , Cruciform Building, Gower Street , London , WC1E 6BT , UK . ; Tel: +44 (0)20 7679 6971
| | - Sarah Frew
- Alzheimer's Research UK UCL Drug Discovery Institute , University College London , Cruciform Building, Gower Street , London , WC1E 6BT , UK . ; Tel: +44 (0)20 7679 6971
| | - Amy Monaghan
- Alzheimer's Research UK UCL Drug Discovery Institute , University College London , Cruciform Building, Gower Street , London , WC1E 6BT , UK . ; Tel: +44 (0)20 7679 6971
| | - Svend Kjær
- The Francis Crick Institute , 1 Midland Road , London , NW1 1AT , UK
| | - Magda Bictash
- Alzheimer's Research UK UCL Drug Discovery Institute , University College London , Cruciform Building, Gower Street , London , WC1E 6BT , UK . ; Tel: +44 (0)20 7679 6971
| | - E Yvonne Jones
- Division of Structural Biology , Wellcome Centre for Human Genetics , University of Oxford , The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive , Oxford , OX3 7BN , UK . ; Tel: +44 (0)1865 287 546
| | - Paul V Fish
- Alzheimer's Research UK UCL Drug Discovery Institute , University College London , Cruciform Building, Gower Street , London , WC1E 6BT , UK . ; Tel: +44 (0)20 7679 6971
- The Francis Crick Institute , 1 Midland Road , London , NW1 1AT , UK
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20
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Gebrelibanos Hiben M, de Haan L, Spenkelink B, Wesseling S, Louisse J, Vervoort J, Rietjens IMCM. Effects of Maerua subcordata (Gilg) DeWolf on electrophile-responsive element (EpRE)-mediated gene expression in vitro. PLoS One 2019; 14:e0215155. [PMID: 30986264 PMCID: PMC6464171 DOI: 10.1371/journal.pone.0215155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 03/27/2019] [Indexed: 01/11/2023] Open
Abstract
Plant extracts and phytochemicals may prevent chronic diseases via activation of adaptive cellular stress response pathways including induction of antioxidant and phase II detoxifying enzymes. The regulatory regions of these inducible genes encode the electrophile-response element (EpRE). This study tested the EpRE induction ability of Maerua subcordata (fruit, leaf, root, seed) methanol extracts and selected candidate constituents thereof, identified by liquid chromatography coupled with multistage mass spectroscopy, employing an EpRE luciferase reporter gene assay using hepa-1c1c7 mouse hepatoma cells. A parallel Cytotox CALUX assay using human osteosarcoma U2OS cells was used to monitor any non-specific changes in luciferase activity or cytotoxicity. Results showed that fruit, root, and seed extracts were non-cytotoxic up to a concentration of 30 gram dry weight per litre but the leaf extract exhibited some cytotoxicity and that the leaf (despite some cytotoxicity), fruit, and seed extracts showed strong induction of EpRE mediated gene expression while induction by the root extract was minimal. Selected candidates included glucosinolates, isothiocyanates, and some biogenic amines. Subsequent studies showed that methyl-, ethyl-, isopropyl-, isobutyl- isothiocyanates, and sec-butyl thiocyanate as well as glucobrassicin induced concentration (1–100 μM) dependent EpRE-mediated gene expression while the biogenic amines stachydrine and trigonelline acted as inhibitors of EpRE-mediated gene expression at 100 μM. The identification of glucolepidiin, glucobrassicin, glucocapparin, stachydrine, and trigonelline in all extracts was confirmed using standards and based on multiple reaction monitoring; yet, glucobrassicin level in the root extract was negligible. In conclusion, this study provided a first report on EpRE mediated gene expression effects of M. subcordata; and despite detection of different glucosinolates in all extracts, those containing glucobrassicin particularly displayed high EpRE induction. Because EpRE inducers are cytoprotective and potential chemopreventive agents while inhibitors are suggested adjuvants of chemotherapy, results of this study imply that process manipulation of this plant may result in herbal preparations that may be used as chemopreventive agents or adjuvants of chemotherapies.
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Affiliation(s)
- Mebrahtom Gebrelibanos Hiben
- Division of Toxicology, Wageningen University, WE Wageningen, The Netherlands
- Department of Pharmacognosy, School of Pharmacy, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
- * E-mail: ,
| | - Laura de Haan
- Division of Toxicology, Wageningen University, WE Wageningen, The Netherlands
| | - Bert Spenkelink
- Division of Toxicology, Wageningen University, WE Wageningen, The Netherlands
| | - Sebas Wesseling
- Division of Toxicology, Wageningen University, WE Wageningen, The Netherlands
| | - Jochem Louisse
- Division of Toxicology, Wageningen University, WE Wageningen, The Netherlands
| | - Jacques Vervoort
- Laboratory of Biochemistry, Wageningen University, WE Wageningen, The Netherlands
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21
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Marian CA, Stoszko M, Wang L, Leighty MW, de Crignis E, Maschinot CA, Gatchalian J, Carter BC, Chowdhury B, Hargreaves DC, Duvall JR, Crabtree GR, Mahmoudi T, Dykhuizen EC. Small Molecule Targeting of Specific BAF (mSWI/SNF) Complexes for HIV Latency Reversal. Cell Chem Biol 2018; 25:1443-1455.e14. [PMID: 30197195 PMCID: PMC6404985 DOI: 10.1016/j.chembiol.2018.08.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 05/24/2018] [Accepted: 08/06/2018] [Indexed: 12/19/2022]
Abstract
The persistence of a pool of latently HIV-1-infected cells despite combination anti-retroviral therapy treatment is the major roadblock for a cure. The BAF (mammalian SWI/SNF) chromatin remodeling complex is involved in establishing and maintaining viral latency, making it an attractive drug target for HIV-1 latency reversal. Here we report a high-throughput screen for inhibitors of BAF-mediated transcription in cells and the subsequent identification of a 12-membered macrolactam. This compound binds ARID1A-specific BAF complexes, prevents nucleosomal positioning, and relieves transcriptional repression of HIV-1. Through this mechanism, these compounds are able to reverse HIV-1 latency in an in vitro T cell line, an ex vivo primary cell model of HIV-1 latency, and in patient CD4+ T cells without toxicity or T cell activation. These macrolactams represent a class of latency reversal agents with unique mechanism of action, and can be combined with other latency reversal agents to improve reservoir targeting.
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Affiliation(s)
- Christine A Marian
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Mateusz Stoszko
- Department of Biochemistry, Erasmus University Medical Center, Ee634, P.O. Box 2040, 3000CA Rotterdam, the Netherlands
| | - Lili Wang
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Matthew W Leighty
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Elisa de Crignis
- Department of Biochemistry, Erasmus University Medical Center, Ee634, P.O. Box 2040, 3000CA Rotterdam, the Netherlands
| | - Chad A Maschinot
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Jovylyn Gatchalian
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, CA 92037, USA
| | - Benjamin C Carter
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Basudev Chowdhury
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Diana C Hargreaves
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jeremy R Duvall
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Gerald R Crabtree
- HHMI and the Departments of Developmental Biology and Pathology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA.
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Ee634, P.O. Box 2040, 3000CA Rotterdam, the Netherlands.
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA.
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22
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Tachibana K, Yuzuriha T, Tabata R, Fukuda S, Maegawa T, Takahashi R, Tanimoto K, Tsujino H, Nunomura K, Lin B, Matsuura Y, Tanaka T, Hamakubo T, Sakai J, Kodama T, Kobayashi T, Ishimoto K, Miyachi H, Doi T. Discovery of peroxisome proliferator-activated receptor α (PPARα) activators with a ligand-screening system using a human PPARα-expressing cell line. J Biol Chem 2018; 293:10333-10343. [PMID: 29764933 DOI: 10.1074/jbc.ra118.002077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/04/2018] [Indexed: 11/06/2022] Open
Abstract
Peroxisome proliferator-activated receptor α (PPARα) is a ligand-activated transcription factor that belongs to the superfamily of nuclear hormone receptors. PPARα is mainly expressed in the liver, where it activates fatty acid oxidation and lipoprotein metabolism and improves plasma lipid profiles. Therefore, PPARα activators are often used to treat patients with dyslipidemia. To discover additional PPARα activators as potential compounds for use in hypolipidemic drugs, here we established human hepatoblastoma cell lines with luciferase reporter expression from the promoters containing peroxisome proliferator-responsive elements (PPREs) and tetracycline-regulated expression of full-length human PPARα to quantify the effects of chemical ligands on PPARα activity. Using the established cell-based PPARα-activator screening system to screen a library of >12,000 chemical compounds, we identified several hit compounds with basic chemical skeletons different from those of known PPARα agonists. One of the hit compounds, a 1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid derivative we termed compound 3, selectively up-regulated PPARα transcriptional activity, leading to PPARα target gene expression both in vitro and in vivo Of note, the half-maximal effective concentrations of the hit compounds were lower than that of the known PPARα ligand fenofibrate. Finally, fenofibrate or compound 3 treatment of high fructose-fed rats having elevated plasma triglyceride levels for 14 days indicated that compound 3 reduces plasma triglyceride levels with similar efficiency as fenofibrate. These observations raise the possibility that 1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid derivatives might be effective drug candidates for selective targeting of PPARα to manage dyslipidemia.
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Affiliation(s)
- Keisuke Tachibana
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871,
| | - Tomohiro Yuzuriha
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871.,the Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101
| | - Ryotaro Tabata
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871
| | - Syohei Fukuda
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871
| | - Takashi Maegawa
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871
| | - Rika Takahashi
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871
| | - Keiichi Tanimoto
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871
| | - Hirofumi Tsujino
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871
| | - Kazuto Nunomura
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871
| | - Bangzhong Lin
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871
| | - Yoshiharu Matsuura
- the Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871
| | | | - Takao Hamakubo
- the Department of Quantitative Biology and Medicine, and
| | - Juro Sakai
- the Division of Metabolic Medicine, Research Center for Advanced Science and Technology, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, and
| | | | - Tadayuki Kobayashi
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871
| | - Kenji Ishimoto
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871
| | - Hiroyuki Miyachi
- the Lead Exploration Unit, Drug Discovery Initiative, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Takefumi Doi
- From the Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871,
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23
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Bain PA, Kumar A. In vitro nuclear receptor inhibition and cytotoxicity of hydraulic fracturing chemicals and their binary mixtures. CHEMOSPHERE 2018; 198:565-573. [PMID: 29433907 DOI: 10.1016/j.chemosphere.2017.12.057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/27/2017] [Accepted: 12/09/2017] [Indexed: 06/08/2023]
Abstract
The widespread use of hydraulic fracturing (HF) in oil and gas extraction operations has led to concern over environmental risks posed by chemicals used in HF fluids. Here we employed a suite of stable luciferase reporter gene assays to investigate the potential for selected HF chemicals or geogenics to activate or antagonise nuclear receptor signalling. We screened three biocides (bronopol [BP], glutaraldehyde [GA], and tetrakis(hydroxymethyl)phosphonium sulfate [THPS]), a surfactant (2-butoxyethanol), a friction reducer (polyacrylamide), and a coal seam geogenic (o-cresol) for their potential to act as agonists or antagonists of the estrogen receptor, androgen receptor, progesterone receptor (PR), glucocorticoid receptor or peroxisome proliferator-activated receptor gamma (PPARγ). None of the chemicals induced luciferase activity in any of assays used in the study. In antagonistic mode, BP, GA and THPS caused reductions in luciferase activity in the reporter assays at higher concentrations (50-100 μM), while at low concentrations (2-10 μM) GA and THPS enhanced luciferase activity in some assays relative to controls. None of the other tested chemicals exhibited antagonism in the selected assays. In most cases, altered receptor signalling only occurred at concentrations exhibiting cytotoxicity. However, PPARγ activity, and to a lesser extent PR activity, were inhibited by THPS at sub-cytotoxic concentrations. The majority of binary combinations tested exhibited significantly less-than-additive cytotoxicity, and none of the combinations exhibited synergistic cytotoxicity. In summary, the results of the present study indicate that the selected chemicals are not likely to function as direct agonists of the nuclear receptors tested, and only one chemical, THPS was an apparent partial antagonist of two nuclear receptors.
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Affiliation(s)
- Peter A Bain
- CSIRO Land & Water, Locked bag 2, Glen Osmond, SA 5064, Australia.
| | - Anu Kumar
- CSIRO Land & Water, Locked bag 2, Glen Osmond, SA 5064, Australia.
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24
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Auld DS, Narahari J, Ho PI, Casalena D, Nguyen V, Cirbaite E, Hughes D, Daly J, Webb B. Characterization and Use of TurboLuc Luciferase as a Reporter for High-Throughput Assays. Biochemistry 2018; 57:4700-4706. [PMID: 29641191 DOI: 10.1021/acs.biochem.8b00290] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Luciferase-based reporter assays are powerful tools for monitoring gene expression in cells because of their ultrasensitive detection capacity and wide dynamic range. Here we describe the characterization and use of a luciferase reporter enzyme derived from the marine copepod Metridia luciferase family, referred to as TurboLuc luciferase (TurboLuc). To develop TurboLuc, the wild-type luciferase was modified to decrease its size, increase brightness, slow luminescent signal decay, and provide for efficient intracellular expression. To determine the enzyme susceptibility to compound inhibition and judge the suitability of using of TurboLuc as a reporter in screening assays, purified TurboLuc enzyme was screened for inhibitors using two different compound libraries. No inhibitors of this enzyme were identified in a library representative of typical diverse low molecular weight (LMW) compounds using a purified TurboLuc enzyme assay supporting that such libraries will show very low interference with this enzyme. We were able to identify a few inhibitors from a purified natural product library which can serve as useful tools to validate assays using TurboLuc. In addition to the inhibitor profile for TurboLuc we describe the use of this reporter in cells employing miniaturized assay volumes within 1536-well plates. TurboLuc luciferase is the smallest luciferase reporter enzyme described to date (16 kDa), shows bright luminescence and low interference by LMW compounds, and therefore should provide an ideal reporter in assays applied to high-throughput screening.
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Affiliation(s)
- Douglas S Auld
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts , United States
| | - Janaki Narahari
- Thermo Fisher Scientific , Rockford , Illinois , United States
| | - Pei-I Ho
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts , United States
| | - Dominick Casalena
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts , United States
| | - Vy Nguyen
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts , United States
| | | | - Doug Hughes
- Thermo Fisher Scientific , Rockford , Illinois , United States
| | - John Daly
- Gene Stream Pty Ltd , Perth , Australia
| | - Brian Webb
- Thermo Fisher Scientific , Rockford , Illinois , United States
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25
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Prinsloo G, Marokane CK, Street RA. Anti-HIV activity of southern African plants: Current developments, phytochemistry and future research. JOURNAL OF ETHNOPHARMACOLOGY 2018; 210:133-155. [PMID: 28807850 PMCID: PMC7125770 DOI: 10.1016/j.jep.2017.08.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 05/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The African continent is home to a large number of higher plant species used over centuries for many applications, which include treating and managing diseases such as HIV. Due to the overwhelming prevalence and incidence rates of HIV, especially in sub-Saharan Africa, it is necessary to develop new and affordable treatments. AIM OF THE STUDY The article provides an extensive overview of the status on investigation of plants from the southern African region with ethnobotanical use for treating HIV or HIV-related symptoms, or the management of HIV. The review also provide an account of the in vitro assays, anti-viral activity and phytochemistry of these plants. MATERIALS AND METHODS Peer-reviewed articles investigating plants with ethnobotanical information for the treatment or management of HIV or HIV-related symptoms from the southern African region were acquired from Science Direct, PubMed central and Google Scholar. The selection criteria was that (1) plants should have a record of traditional/popular use for infectious or viral diseases, HIV treatment or symptoms similar to HIV infection, (2) if not traditionally/popularly used, plants should be closely related to plants with popular use and HIV activity identified by means of in vitro assays, (3) plants should have been identified scientifically, (4) should be native to southern African region and (5) anti-HIV activity should be within acceptable ranges. RESULTS Many plants in Africa and specifically the southern African region have been used for the treatment of HIV or HIV related symptoms and have been investigated suing various in vitro techniques. In vitro assays using HIV enzymes such as reverse transcriptase (RT), integrase (IN) and protease (PR), proteins or cell-based assays have been employed to validate the use of these plants with occasional indication of the selectivity index (SI) or therapeutic index (TI), with only one study, that progressed to in vivo testing. The compounds identified from plants from southern Africa is similar to compounds identified from other regions of the world, and the compounds have been divided into three groups namely (1) flavonoids and flavonoid glycosides, (2) terpenoids and terpenoid glycosides and (3) phenolic acids and their conjugated forms. CONCLUSIONS An investigation of the plants from southern Africa with ethnobotanical use for the treatment of HIV, management of HIV or HIV-related symptoms, therefore provide a very good analysis of the major assays employed and the anti-viral compounds and compound groups identified. The similarity in identified anti-viral compounds worldwide should support the progression from in vitro studies to in vivo testing in development of affordable and effective anti-HIV agents for countries with high infection and mortality rates due to HIV/AIDS.
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Affiliation(s)
- Gerhard Prinsloo
- Department of Agriculture and Animal health, University of South Africa (UNISA), Florida Campus, Florida 1710, South Africa.
| | - Cynthia K Marokane
- Department of Agriculture and Animal health, University of South Africa (UNISA), Florida Campus, Florida 1710, South Africa.
| | - Renée A Street
- Environment and Health Research Unit, South African Medical Research Council, Durban 4041, South Africa; Department of Occupational and Environmental Health, University of KwaZulu-Natal, Durban 4001, South Africa.
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26
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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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27
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Rheiner S, Reichel D, Rychahou P, Izumi T, Yang HS, Bae Y. Polymer nanoassemblies with hydrophobic pendant groups in the core induce false positive siRNA transfection in luciferase reporter assays. Int J Pharm 2017. [PMID: 28629980 DOI: 10.1016/j.ijpharm.2017.06.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Poly(ethylene glycol)-conjugated polyethylenimine (PEG-PEI) is a widely studied cationic polymer used to develop non-viral vectors for siRNA therapy of genetic disorders including cancer. Cell lines stably expressing luciferase reporter protein typically evaluate the transfection efficacy of siRNA/PEG-PEI complexes, however recent findings revealed that PEG-PEI can reduce luciferase expression independent of siRNA. This study elucidates a cause of the false positive effect in luciferase assays by using polymer nanoassemblies (PNAs) made from PEG, PEI, poly-(l-lysine) (PLL), palmitate (PAL), and deoxycholate (DOC): PEG-PEI (2P), PEG-PEI-PAL (3P), PEG-PLL (2P'), PEG-PLL-PAL (3P'), and PEG-PEI-DOC (2PD). In vitro transfection and western blot assays of luciferase using a colorectal cancer cell line expressing luciferase (HT29/LUC) concluded that 2P and 2P' caused no luciferase expression reduction while hydrophobically modified PNAs induced a 35-50% reduction (3P'<2PD<3P). Although cell viability remained stagnant, 3P triggered cellular stress responses including increased membrane porosity and decreased ATP and cellular protein concentrations. Raman spectroscopy suggested that hydrophobic groups influence PNA conformation changes, which may have caused over-ubiquitination and degradation of luciferase in the cells. These results indicate that hydrophobically modified PEG-PEI induces cellular distress causing over-ubiquitination of the luciferase protein, producing false positive siRNA transfection in the luciferase assay.
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Affiliation(s)
- Steven Rheiner
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536, USA
| | - Derek Reichel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536, USA
| | - Piotr Rychahou
- Markey Cancer Center, University of Kentucky, 800 Rose Street, CC140, Lexington, KY 40536, USA; Department of Surgery, College of Medicine, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA
| | - Tadahide Izumi
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, 1095 V.A. Drive, Lexington, KY 40536, USA
| | - Hsin-Sheng Yang
- Markey Cancer Center, University of Kentucky, 800 Rose Street, CC140, Lexington, KY 40536, USA; Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, 1095 V.A. Drive, Lexington, KY 40536, USA
| | - Younsoo Bae
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536, USA.
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28
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Two low complexity ultra-high throughput methods to identify diverse chemically bioactive molecules using Saccharomyces cerevisiae. Microbiol Res 2017; 199:10-18. [DOI: 10.1016/j.micres.2017.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/17/2017] [Accepted: 02/19/2017] [Indexed: 11/21/2022]
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29
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Prinsloo G, Papadi G, Hiben MG, de Haan L, Louisse J, Beekmann K, Vervoort J, Rietjens IMCM. In vitro bioassays to evaluate beneficial and adverse health effects of botanicals: promises and pitfalls. Drug Discov Today 2017; 22:1187-1200. [PMID: 28533190 DOI: 10.1016/j.drudis.2017.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/24/2017] [Accepted: 05/09/2017] [Indexed: 01/05/2023]
Abstract
This review provides an update on the promises and pitfalls when using in vitro bioassays to evaluate beneficial and adverse health effects of botanicals and botanical preparations. Important issues addressed in the paper are: (i) the type of assays and biological effects available; (ii) false-positives, false-negatives and confounding factors; (iii) matrix and combination effects; (iv) extrapolation of in vitro data to the in vivo situation; (v) when (not) to use bioassays; and (vi) identification of active constituents. It is concluded that in vitro bioassays provide models to detect beneficial as well as adverse activities, but that linking these observations to individual ingredients and extrapolations to the in vivo situation is more complicated than generally anticipated.
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Affiliation(s)
- Gerhard Prinsloo
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; Department of Agriculture and Animal Health, University of South Africa, Private bag x 6, Florida, South Africa.
| | - Georgia Papadi
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; Department of Biological Applications & Technology, University of Ioannina, Greece
| | - Mebrahtom G Hiben
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; Department of Pharmacognosy, School of Pharmacy, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | - Laura de Haan
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jochem Louisse
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Karsten Beekmann
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jacques Vervoort
- Department of Agriculture and Animal Health, University of South Africa, Private bag x 6, Florida, South Africa; Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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30
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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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31
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Cevenini L, Calabretta MM, Lopreside A, Branchini BR, Southworth TL, Michelini E, Roda A. Bioluminescence Imaging of Spheroids for High‐throughput Longitudinal Studies on 3D Cell Culture Models. Photochem Photobiol 2017; 93:531-535. [DOI: 10.1111/php.12718] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/11/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Luca Cevenini
- Department of Chemistry “G. Ciamician” University of Bologna Bologna Italy
| | | | - Antonia Lopreside
- Department of Chemistry “G. Ciamician” University of Bologna Bologna Italy
| | | | | | - Elisa Michelini
- Department of Chemistry “G. Ciamician” University of Bologna Bologna Italy
- Health Sciences and Technologies‐Interdepartmental Center for Industrial Research (HST‐ICIR) University of Bologna Bologna Italy
- INBB, Istituto Nazionale di Biostrutture e Biosistemi Roma Italy
| | - Aldo Roda
- Department of Chemistry “G. Ciamician” University of Bologna Bologna Italy
- INBB, Istituto Nazionale di Biostrutture e Biosistemi Roma Italy
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32
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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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33
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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: 144] [Impact Index Per Article: 18.0] [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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34
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Becker JP, Clemens JR, Theile D, Weiss J. Bortezomib and ixazomib protect firefly luciferase from degradation and can flaw respective reporter gene assays. Anal Biochem 2016; 509:124-129. [DOI: 10.1016/j.ab.2016.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/09/2016] [Accepted: 06/09/2016] [Indexed: 12/11/2022]
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35
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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: 29] [Impact Index Per Article: 3.6] [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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36
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Seeger B, Klawonn F, Nguema Bekale B, Steinberg P. Mixture Effects of Estrogenic Pesticides at the Human Estrogen Receptor α and β. PLoS One 2016; 11:e0147490. [PMID: 26812056 PMCID: PMC4728068 DOI: 10.1371/journal.pone.0147490] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/05/2016] [Indexed: 11/18/2022] Open
Abstract
Consumers of fruits and vegetables are frequently exposed to small amounts of hormonally active pesticides, some of them sharing a common mode of action such as the activation of the human estrogen receptor α (hERα) or β (hERβ). Therefore, it is of particular importance to evaluate risks emanating from chemical mixtures, in which the individual pesticides are present at human-relevant concentrations, below their corresponding maximum residue levels. Binary and ternary iso-effective mixtures of estrogenic pesticides at effect concentrations eliciting a 1 or 10% effect in the presence or absence of 17β-estradiol were tested experimentally at the hERα in the yeast-based estrogen screen (YES) assay as well as in the human U2-OS cell-based ERα chemical-activated luciferase gene expression (ERα CALUX) assay and at the hERβ in the ERβ CALUX assay. The outcome was then compared to predictions calculated by means of concentration addition. In most cases, additive effects were observed with the tested combinations in all three test systems, an observation that supports the need to expand the risk assessment of pesticides and consider cumulative risk assessment. An additional testing of mixture effects at the hERβ showed that most test substances being active at the hERα could also elicit additive effects at the hERβ, but the hERβ was less sensitive. In conclusion, effects of the same ligands at the hERα and the hERβ could influence the estrogenic outcome under physiological conditions.
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Affiliation(s)
- Bettina Seeger
- Institute for Food Toxicology and Analytical Chemistry, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - Frank Klawonn
- Biostatistics Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
- Department of Computer Science, Ostfalia University of Applied Sciences, Salzdahlumerstr. 46/48, 38302, Wolfenbüttel, Germany
| | - Boris Nguema Bekale
- Department of Computer Science, Ostfalia University of Applied Sciences, Salzdahlumerstr. 46/48, 38302, Wolfenbüttel, Germany
| | - Pablo Steinberg
- Institute for Food Toxicology and Analytical Chemistry, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
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37
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Judson RS, Magpantay FM, Chickarmane V, Haskell C, Tania N, Taylor J, Xia M, Huang R, Rotroff DM, Filer DL, Houck KA, Martin MT, Sipes N, Richard AM, Mansouri K, Setzer RW, Knudsen TB, Crofton KM, Thomas RS. Integrated Model of Chemical Perturbations of a Biological Pathway Using 18 In Vitro High-Throughput Screening Assays for the Estrogen Receptor. Toxicol Sci 2015; 148:137-54. [PMID: 26272952 DOI: 10.1093/toxsci/kfv168] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We demonstrate a computational network model that integrates 18 in vitro, high-throughput screening assays measuring estrogen receptor (ER) binding, dimerization, chromatin binding, transcriptional activation, and ER-dependent cell proliferation. The network model uses activity patterns across the in vitro assays to predict whether a chemical is an ER agonist or antagonist, or is otherwise influencing the assays through a manner dependent on the physics and chemistry of the technology platform ("assay interference"). The method is applied to a library of 1812 commercial and environmental chemicals, including 45 ER positive and negative reference chemicals. Among the reference chemicals, the network model correctly identified the agonists and antagonists with the exception of very weak compounds whose activity was outside the concentration range tested. The model agonist score also correlated with the expected potency class of the active reference chemicals. Of the 1812 chemicals evaluated, 111 (6.1%) were predicted to be strongly ER active in agonist or antagonist mode. This dataset and model were also used to begin a systematic investigation of assay interference. The most prominent cause of false-positive activity (activity in an assay that is likely not due to interaction of the chemical with ER) is cytotoxicity. The model provides the ability to prioritize a large set of important environmental chemicals with human exposure potential for additional in vivo endocrine testing. Finally, this model is generalizable to any molecular pathway for which there are multiple upstream and downstream assays available.
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Affiliation(s)
- Richard S Judson
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711;
| | | | - Vijay Chickarmane
- Division of Biology, California Institute of Technology, Pasadena, California 91125
| | - Cymra Haskell
- §Department of Mathematics, University of Southern California, Los Angeles, California 90089
| | - Nessy Tania
- Department of Mathematics, Smith College, Northampton, Massachusetts 01063
| | - Jean Taylor
- Courant Institute, New York University, New York New York 10012
| | - Menghang Xia
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, Rockville, Maryland 20892
| | - Ruili Huang
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, Rockville, Maryland 20892
| | - Daniel M Rotroff
- Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27607
| | - Dayne L Filer
- **ORISE Fellow at the U.S. EPA, Research Triangle Park, North Carolina 27711
| | - Keith A Houck
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Matthew T Martin
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Nisha Sipes
- NIH National Toxicology Program, Research Triangle Park, North Carolina 27711
| | - Ann M Richard
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Kamel Mansouri
- **ORISE Fellow at the U.S. EPA, Research Triangle Park, North Carolina 27711
| | - R Woodrow Setzer
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Thomas B Knudsen
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Kevin M Crofton
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Russell S Thomas
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
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38
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Auld DS, Davis CA, Jimenez M, Knight S, Orme JP. Examining Ligand-Based Stabilization of Proteins in Cells with MEK1 Kinase Inhibitors. Assay Drug Dev Technol 2015; 13:266-76. [DOI: 10.1089/adt.2014.614] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Douglas S. Auld
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, Massachusetts
| | - Christopher A. Davis
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, Massachusetts
| | - Marta Jimenez
- Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Cambridge, Massachusetts
| | - Sinead Knight
- AstraZeneca, R&D, Innovative Medicines, Macclesfield, Cheshire, United Kingdom
| | - Jonathon P. Orme
- AstraZeneca, R&D, Innovative Medicines, Macclesfield, Cheshire, United Kingdom
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39
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Hasson SA, Fogel AI, Wang C, MacArthur R, Guha R, Heman-Ackah S, Martin S, Youle RJ, Inglese J. Chemogenomic profiling of endogenous PARK2 expression using a genome-edited coincidence reporter. ACS Chem Biol 2015; 10:1188-97. [PMID: 25689131 PMCID: PMC9927027 DOI: 10.1021/cb5010417] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Parkin, an E3 ubiquitin ligase, is a central mediator of mitochondrial quality control and is linked to familial forms of Parkinson's disease (PD). Removal of dysfunctional mitochondria from the cell by Parkin is thought to be neuroprotective, and pharmacologically increasing Parkin levels may be a novel therapeutic approach. We used genome-editing to integrate a coincidence reporter into the PARK2 gene locus of a neuroblastoma-derived cell line and developed a quantitative high-throughput screening (qHTS) assay capable of accurately detecting subtle compound-mediated increases in endogenous PARK2 expression. Interrogation of a chemogenomic library revealed diverse chemical classes that up-regulate the PARK2 transcript, including epigenetic agents, drugs controlling cholesterol biosynthesis, and JNK inhibitors. Use of the coincidence reporter eliminated wasted time pursuing reporter-biased false positives accounting for ∼2/3 of the actives and, coupled with titration-based screening, greatly improves the efficiency of compound selection. This approach represents a strategy to revitalize reporter-gene assays for drug discovery.
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Affiliation(s)
- Samuel A. Hasson
- National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892,These authors contributed equally
| | - Adam I. Fogel
- National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892,These authors contributed equally
| | - Chunxin Wang
- National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892
| | - Ryan MacArthur
- National Center for Advancing Translational Sciences, Rockville, MD 20850
| | - Rajarshi Guha
- National Center for Advancing Translational Sciences, Rockville, MD 20850
| | - Sabrina Heman-Ackah
- NIH Center for Regenerative Medicine, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland 20892
| | - Scott Martin
- National Center for Advancing Translational Sciences, Rockville, MD 20850
| | - Richard J. Youle
- National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892
| | - James Inglese
- National Center for Advancing Translational Sciences, Rockville, MD 20850,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892,To whom correspondence should be addressed. , Phone: 301-217-5723, Fax: 301-217-5736
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40
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Kroeze WK, Sassano MF, Huang XP, Lansu K, McCorvy JD, Giguère PM, Sciaky N, Roth BL. PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome. Nat Struct Mol Biol 2015; 22:362-9. [PMID: 25895059 PMCID: PMC4424118 DOI: 10.1038/nsmb.3014] [Citation(s) in RCA: 480] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/25/2015] [Indexed: 01/14/2023]
Abstract
G protein-coupled receptors (GPCRs) are essential mediators of cellular signaling and are important targets of drug action. Of the approximately 350 nonolfactory human GPCRs, more than 100 are still considered to be 'orphans' because their endogenous ligands remain unknown. Here, we describe a unique open-source resource that allows interrogation of the druggable human GPCRome via a G protein-independent β-arrestin-recruitment assay. We validate this unique platform at more than 120 nonorphan human GPCR targets, demonstrate its utility for discovering new ligands for orphan human GPCRs and describe a method (parallel receptorome expression and screening via transcriptional output, with transcriptional activation following arrestin translocation (PRESTO-Tango)) for the simultaneous and parallel interrogation of the entire human nonolfactory GPCRome.
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Affiliation(s)
- Wesley K Kroeze
- 1] Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [2] National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Maria F Sassano
- 1] Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [2] National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Xi-Ping Huang
- 1] Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [2] National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katherine Lansu
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - John D McCorvy
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Patrick M Giguère
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Noah Sciaky
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Bryan L Roth
- 1] Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [2] National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [3] Program in Neuroscience, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [4] Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
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41
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Kroeze WK, Sassano MF, Huang XP, Lansu K, McCorvy JD, Giguère PM, Sciaky N, Roth BL. PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome. Nat Struct Mol Biol 2015; 22:362-369. [PMID: 25895059 DOI: 10.1021/acscentsci.2c00442/suppl_file/oc2c00442_si_001.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/25/2015] [Indexed: 05/23/2023]
Abstract
G protein-coupled receptors (GPCRs) are essential mediators of cellular signaling and are important targets of drug action. Of the approximately 350 nonolfactory human GPCRs, more than 100 are still considered to be 'orphans' because their endogenous ligands remain unknown. Here, we describe a unique open-source resource that allows interrogation of the druggable human GPCRome via a G protein-independent β-arrestin-recruitment assay. We validate this unique platform at more than 120 nonorphan human GPCR targets, demonstrate its utility for discovering new ligands for orphan human GPCRs and describe a method (parallel receptorome expression and screening via transcriptional output, with transcriptional activation following arrestin translocation (PRESTO-Tango)) for the simultaneous and parallel interrogation of the entire human nonolfactory GPCRome.
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Affiliation(s)
- Wesley K Kroeze
- 1] Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [2] National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Maria F Sassano
- 1] Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [2] National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Xi-Ping Huang
- 1] Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [2] National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katherine Lansu
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - John D McCorvy
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Patrick M Giguère
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Noah Sciaky
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Bryan L Roth
- 1] Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [2] National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [3] Program in Neuroscience, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. [4] Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
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42
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A cell-based high-throughput screen for novel chemical inducers of fetal hemoglobin for treatment of hemoglobinopathies. PLoS One 2014; 9:e107006. [PMID: 25225870 PMCID: PMC4165891 DOI: 10.1371/journal.pone.0107006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/04/2014] [Indexed: 11/19/2022] Open
Abstract
Decades of research have established that the most effective treatment for sickle cell disease (SCD) is increased fetal hemoglobin (HbF). Identification of a drug specific for inducing γ-globin expression in pediatric and adult patients, with minimal off-target effects, continues to be an elusive goal. One hurdle has been an assay amenable to a high-throughput screen (HTS) of chemicals that displays a robust γ-globin off-on switch to identify potential lead compounds. Assay systems developed in our labs to understand the mechanisms underlying the γ- to β-globin gene expression switch during development has allowed us to generate a cell-based assay that was adapted for a HTS of 121,035 compounds. Using chemical inducer of dimerization (CID)-dependent bone marrow cells (BMCs) derived from human γ-globin promoter-firefly luciferase β-globin promoter-Renilla luciferase β-globin yeast artificial chromosome (γ-luc β-luc β-YAC) transgenic mice, we were able to identify 232 lead chemical compounds that induced γ-globin 2-fold or higher, with minimal or no β-globin induction, minimal cytotoxicity and that did not directly influence the luciferase enzyme. Secondary assays in CID-dependent wild-type β-YAC BMCs and human primary erythroid progenitor cells confirmed the induction profiles of seven of the 232 hits that were cherry-picked for further analysis.
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43
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Paley MA, Prescher JA. Bioluminescence: a versatile technique for imaging cellular and molecular features. MEDCHEMCOMM 2014; 5:255-267. [PMID: 27594981 PMCID: PMC5006753 DOI: 10.1039/c3md00288h] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioluminescence is a ubiquitous imaging modality for visualizing biological processes in vivo. This technique employs visible light and interfaces readily with most cell and tissue types, making it a versatile technology for preclinical studies. Here we review basic bioluminescence imaging principles, along with applications of the technology that are relevant to the medicinal chemistry community. These include noninvasive cell tracking experiments, analyses of protein function, and methods to visualize small molecule metabolites. In each section, we also discuss how bioluminescent tools have revealed insights into experimental therapies and aided drug discovery. Last, we highlight the development of new bioluminescent tools that will enable more sensitive and multi-component imaging experiments and, thus, expand our broader understanding of living systems.
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Affiliation(s)
- Miranda A. Paley
- Department of Chemistry, University of California, Irvine, CA, USA
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
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44
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Chen F, Liu SS, Duan XT, Xiao QF. Predicting the mixture effects of three pesticides by integrating molecular simulation with concentration addition modeling. RSC Adv 2014. [DOI: 10.1039/c4ra02698e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Molecular simulation techniques are used to identify the mode of inhibition of chemicals at the ligand–receptor level.
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Affiliation(s)
- Fu Chen
- Key Laboratory of Yangtze River Water Environment
- Ministry of Education, College of Environmental Science and Engineering
- Tongji University
- Shanghai 200092, PR China
| | - Shu-Shen Liu
- Key Laboratory of Yangtze River Water Environment
- Ministry of Education, College of Environmental Science and Engineering
- Tongji University
- Shanghai 200092, PR China
- State Key Laboratory of Pollution Control and Resource Reuse
| | - Xin-Tian Duan
- Key Laboratory of Yangtze River Water Environment
- Ministry of Education, College of Environmental Science and Engineering
- Tongji University
- Shanghai 200092, PR China
| | - Qian-Fen Xiao
- Key Laboratory of Yangtze River Water Environment
- Ministry of Education, College of Environmental Science and Engineering
- Tongji University
- Shanghai 200092, PR China
- State Key Laboratory of Pollution Control and Resource Reuse
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45
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Connelly CM, Deiters A. Identification of inhibitors of microRNA function from small molecule screens. Methods Mol Biol 2014; 1095:147-56. [PMID: 24166310 DOI: 10.1007/978-1-62703-703-7_12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Aberrant expression of microRNAs (miRNAs) has been linked to many human diseases including cancer, immune disorders, heart disease, and viral infections. Thus, small molecule inhibitors of miRNAs have potential as new therapeutic agents, as probes for the elucidation of detailed mechanisms of miRNA function, and as tools for the discovery of new targets for the treatment of human diseases. In order to identify small molecule inhibitors of specific miRNAs, functional assays have been developed and applied to the screening of small molecule libraries. Here, we report the application of a luciferase-based reporter assay of miRNA miR-122 function to the discovery of small molecule miR-122 inhibitors.
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Affiliation(s)
- Colleen M Connelly
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
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Abstract
Over the last three decades, imaging has been a thriving field with continuous egression of more reliable and highly sophisticated tools and techniques allowing better understanding of biological processes in living organisms. This field continues to expand and its applications broaden to encompass limitless applications in various biomedical research areas. It is however, of utmost importance to understand the capabilities and limitations of this technique as new challenges and hurdles continue to arise. This chapter describes the general properties of bioluminescence imaging and commonly used reporters while underlining the challenges and limitations with these modalities.
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Affiliation(s)
- Christian E Badr
- Experimental Therapeutics and Molecular Imaging Laboratory, Department of Neurology, Neuroscience Center, Massachusetts General Hospital, Boston, MA, USA
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47
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van der Linden SC, von Bergh ARM, van Vught-Lussenburg BMA, Jonker LRA, Teunis M, Krul CAM, van der Burg B. Development of a panel of high-throughput reporter-gene assays to detect genotoxicity and oxidative stress. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 760:23-32. [PMID: 24362253 DOI: 10.1016/j.mrgentox.2013.09.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 08/13/2013] [Accepted: 09/28/2013] [Indexed: 12/22/2022]
Abstract
The lack of toxicological information on many of the compounds that humans use or are exposed to, intentionally or unintentionally, poses a big problem in risk assessment. To fill this data gap, more emphasis is given to fast in vitro screening tools that can add toxicologically relevant information regarding the mode(s) of action via which compounds can elicit adverse effects, including genotoxic effects. By use of bioassays that can monitor the activation of specific cellular signalling pathways, many compounds can be screened in a high-throughput manner. We have developed two new specific reporter-gene assays that can monitor the effects of compounds on two pathways of interest: the p53 pathway (p53 CALUX) for genotoxicity and the Nrf2 pathway (Nrf2 CALUX) for oxidative stress. To exclude non-specific effects by compounds influencing the luciferase reporter-gene expression non-specifically, a third assay was developed to monitor changes in luciferase expression by compounds in general (Cytotox CALUX). To facilitate interpretation of the data and to avoid artefacts, all three reporter-gene assays used simple and defined reporter genes and a similar cellular basis, the human U2OS cell line. The three cell lines were validated with a range of reference compounds including genotoxic and non-genotoxic agents. The sensitivity (95%) and specificity (85%) of the p53 CALUX was high, showing that the assay is able to identify various types of genotoxic compound, while avoiding the detection of false positives. The Nrf2 CALUX showed specific responses to oxidants only, enabling the identification of compounds that elicit part of their genotoxicity via oxidative stress. All reporter-gene assays can be used in a high-throughput screening format and can be supplemented with other U2OS-based reporter-gene assays that can profile nuclear receptor activity, and several other signalling pathways.
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Affiliation(s)
| | - Anne R M von Bergh
- Innovative Testing in Life Sciences and Chemistry, Research Centre Technology & Innovation, University of Applied Sciences Utrecht, The Netherlands
| | | | | | - Marc Teunis
- Innovative Testing in Life Sciences and Chemistry, Research Centre Technology & Innovation, University of Applied Sciences Utrecht, The Netherlands
| | - Cyrille A M Krul
- Innovative Testing in Life Sciences and Chemistry, Research Centre Technology & Innovation, University of Applied Sciences Utrecht, The Netherlands
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48
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Jensen M, Roberts L, Johnson A, Fukushima M, Davis R. Next generation 1536-well oligonucleotide synthesizer with on-the-fly dispense. J Biotechnol 2013; 171:76-81. [PMID: 24355807 DOI: 10.1016/j.jbiotec.2013.11.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 11/21/2013] [Accepted: 11/25/2013] [Indexed: 11/16/2022]
Abstract
Here we report the development of our Next Generation Automated Multiplexed Oligonucleotide Synthesizer (NG-1536-AMOS), capable of producing 1536 samples in a single run using a multi-well filtered titer plate. With the potential to synthesize up to 3456 samples per plate, we converted the BioRAPTR Flying Reagent Dispenser into an open-well system where spent reagents are drained to waste under vacuum. During synthesis, reagents are delivered on-the-fly to each micro-titer well at volumes ≤5 μl with plate speeds up to 150 mm/s. Using gas-phase cleavage and deprotection, a full plate of 1536 60 mers may be processed with same-day turnaround with an average yield per well at 3.5 nmol. Final product at only $0.00277/base is eluted into a low-volume collection plate for immediate use in downstream application (e.g. Biomek FX for versatile sample handling). Also, crude oligonucleotide quality is comparable to that of commercial synthesis instrumentation, with an error rate on the NG-1536-AMOS platform of 1.53/717 bases. Furthermore, mass spectral analysis on strands synthesized up to 80 bases showed high purity with an average coupling efficiency of 99.5%.
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Affiliation(s)
- Michael Jensen
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA.
| | - Lester Roberts
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
| | | | - Marilyn Fukushima
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
| | - Ronald Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
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Holub JM, Larochelle JR, Appelbaum JS, Schepartz A. Improved assays for determining the cytosolic access of peptides, proteins, and their mimetics. Biochemistry 2013; 52:9036-46. [PMID: 24256505 DOI: 10.1021/bi401069g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteins and other macromolecules that cross biological membranes have great potential as tools for research and next-generation therapeutics. Here, we describe two assays that effectively quantify the cytosolic localization of a number of previously reported peptides and protein domains. One assay, which we call GIGI (glucocorticoid-induced eGFP induction), is an amplified assay that informs on relative cytosolic access without the need for sophisticated imaging equipment or adherent cells. The second, GIGT (glucocorticoid-induced eGFP translocation), is a nonamplified assay that informs on relative cytosolic access and exploits sophisticated imaging equipment to facilitate high-content screens in live cells. Each assay was employed to quantify the cytosolic delivery of several canonical "cell permeable peptides," as well as more recently reported minimally cationic miniature proteins and zinc finger nuclease domains. Our results show definitively that both overall charge as well as charge distribution influence cytosolic access and that small protein domains containing a discrete, helical, penta-Arg motif can dramatically improve the cytosolic delivery of small folded proteins such as zinc finger domains. We anticipate that the assays described herein will prove useful to explore and discover the fundamental physicochemical and genetic properties that influence both the uptake and endosomal release of peptidic molecules and their mimetics.
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Affiliation(s)
- Justin M Holub
- Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
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Karaki F, Ohgane K, Dodo K, Hashimoto Y. Structure–activity relationship studies of Niemann-Pick type C1-like 1 (NPC1L1) ligands identified by screening assay monitoring pharmacological chaperone effect. Bioorg Med Chem 2013; 21:5297-309. [DOI: 10.1016/j.bmc.2013.06.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 06/07/2013] [Accepted: 06/08/2013] [Indexed: 11/30/2022]
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