1
|
Sultan F, Basu R, Murthy D, Kochar M, Attri KS, Aggarwal A, Kumari P, Dnyane P, Tanwar J, Motiani RK, Singh A, Gadgil C, Bhavesh NS, Singh PK, Natarajan VT, Gokhale RS. Temporal analysis of melanogenesis identifies fatty acid metabolism as key skin pigment regulator. PLoS Biol 2022; 20:e3001634. [PMID: 35584084 PMCID: PMC9116682 DOI: 10.1371/journal.pbio.3001634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/19/2022] [Indexed: 11/19/2022] Open
Abstract
Therapeutic methods to modulate skin pigmentation has important implications for skin cancer prevention and for treating cutaneous hyperpigmentary conditions. Towards defining new potential targets, we followed temporal dynamics of melanogenesis using a cell-autonomous pigmentation model. Our study elucidates 3 dominant phases of synchronized metabolic and transcriptional reprogramming. The melanogenic trigger is associated with high MITF levels along with rapid uptake of glucose. The transition to pigmented state is accompanied by increased glucose channelisation to anabolic pathways that support melanosome biogenesis. SREBF1-mediated up-regulation of fatty acid synthesis results in a transient accumulation of lipid droplets and enhancement of fatty acids oxidation through mitochondrial respiration. While this heightened bioenergetic activity is important to sustain melanogenesis, it impairs mitochondria lately, shifting the metabolism towards glycolysis. This recovery phase is accompanied by activation of the NRF2 detoxication pathway. Finally, we show that inhibitors of lipid metabolism can resolve hyperpigmentary conditions in a guinea pig UV-tanning model. Our study reveals rewiring of the metabolic circuit during melanogenesis, and fatty acid metabolism as a potential therapeutic target in a variety of cutaneous diseases manifesting hyperpigmentary phenotype. Temporal analysis of melanogenesis, based on transcriptomic and metabolomic signatures, reveals fatty acid metabolism as a crucial mediator of the transition between pigmentation phases. Inhibitors of the fatty acid pathway could represent a new target for modulating pigmentation.
Collapse
Affiliation(s)
- Farina Sultan
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
| | - Reelina Basu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Divya Murthy
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Manisha Kochar
- Immunometabolism Laboratory, National Institute of Immunology, New Delhi, India
| | - Kuldeep S. Attri
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Ayush Aggarwal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
| | - Pooja Kumari
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Pooja Dnyane
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
- CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Jyoti Tanwar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
- Laboratory of Calciomics and Systemic Pathophysiology, Regional Centre of Biotechnology (RCB), Faridabad, Haryana, India
| | - Rajender K. Motiani
- Laboratory of Calciomics and Systemic Pathophysiology, Regional Centre of Biotechnology (RCB), Faridabad, Haryana, India
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
| | - Chetan Gadgil
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
- CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Neel Sarovar Bhavesh
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Pankaj K. Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Vivek T. Natarajan
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
- * E-mail: (VTN); (RSG)
| | - Rajesh S. Gokhale
- Immunometabolism Laboratory, National Institute of Immunology, New Delhi, India
- * E-mail: (VTN); (RSG)
| |
Collapse
|
2
|
Wang Y, Zhou X, Zhao B, Ren X, Chen Y, Si J, Zhou R, Gan L, Zhang H. Early embryonic exposure of ionizing radiations disrupts zebrafish pigmentation. J Cell Physiol 2018; 234:940-949. [PMID: 30144054 DOI: 10.1002/jcp.26922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 06/13/2018] [Indexed: 12/23/2022]
Abstract
Studies have demonstrated that zebrafish are powerful tools for monitoring environmental toxicity, including radiation hazard. Here we investigated the developmental toxicity of ionizing radiation (IR) in an in vivo embryonic zebrafish model. The effects of heavy ion (12 C6+ ), proton, and X-ray radiation on early zebrafish embryos were determined. A similar dose-dependent decrease in the hatch and survival rate of zebrafish embryos was observed after exposure to these irradiations. Exposure of zebrafish embryos to 1-4 Gy IR caused significant loss of pigmentation. Quantitative real-time reverse transcription polymerase chain reaction, western blot analysis, and in situ hybridization (ISH) experiment revealed that atp5α1 was markedly upregulated in irradiated zebrafish embryos. In addition, IR resulted in a rapid decrease in total adenosine triphosphate (ATP) generation. With dual functions of synthesizing or hydrolyzing ATP, ATP synthase regulated H+ transport crossing the mitochondrial inner. Administration of the mitochondrial ATP synthase inhibitor, oligomycin, partially restored pigmentation in irradiated zebrafish embryos, but the ATPase inhibitor, BTB06584, had no effect. Taken together, these results showed that IR exposure downregulated zebrafish pigmentation through regulation of H+ ion transport in mitochondria.
Collapse
Affiliation(s)
- Yupei Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,CAS Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Institute of Modern Physics, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zhou
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Baoquan Zhao
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Peking, China
| | - Xiaotang Ren
- State Key Laboratory of Nuclear Physics and Technology, Peking University, Peking, China
| | - Yuhong Chen
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,CAS Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Institute of Modern Physics, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Si
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,CAS Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Institute of Modern Physics, Lanzhou, China
| | - Rong Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,CAS Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Institute of Modern Physics, Lanzhou, China
| | - Lu Gan
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,CAS Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Institute of Modern Physics, Lanzhou, China
| | - Hong Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,CAS Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Institute of Modern Physics, Lanzhou, China.,Gansu Wuwei Tumor Hospital, Wuwei, China
| |
Collapse
|
3
|
Samat N, Ng MF, Ruslan NF, Okuda KS, Tan PJ, Patel V. Interference Potential of Tannins and Chlorophylls in Zebrafish Phenotypic-Based Assays. Assay Drug Dev Technol 2018; 16:408-419. [PMID: 29985634 DOI: 10.1089/adt.2017.833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Natural products are prolific producers of diverse chemical scaffolds, which have yielded several clinically useful drugs. However, the complex features of natural products present challenges for identifying bioactive molecules using high-throughput screens. For most assays, measured endpoints are either colorimetric or luminescence based. Thus, the presence of the major metabolites, tannins, and chlorophylls, in natural products could potentially interfere with these measurements to give either false-positive or false-negative hits. In this context, zebrafish phenotypic assays provide an alternative approach to bioprospect naturally occurring bioactive compounds. Whether tannins and/or chlorophylls interfere in zebrafish phenotypic assays, is unclear. In this study, we evaluated the interference potential of tannins and chlorophylls against efficacy of known small-molecule inhibitors that are known to cause phenotypic abnormalities in developing zebrafish embryos. First, we fractionated tannin-enriched fraction (TEF) and chlorophyll-enriched fraction (CEF) from Camellia sinensis and cotreated them with PD0325901 [mitogen-activated protein kinase-kinase (MEK) inhibitor] and sunitinib malate (SM; anti-[lymph]angiogenic drug). While TEF and CEF did not interfere with phenotypic or molecular endpoints of PD0325901, TEF at 100 μg/mL partially masked the antiangiogenic effect of SM. On the other hand, CEF (100 μg/mL) was toxic when treated up to 6 dpf. Furthermore, CEF at 100 μg/mL potentially enhanced the activity of γ-secretase inhibitors, resulting in toxicity of treated embryos. Our study provides evidence that the presence of tannin and/or chlorophyll in natural products do interfere with zebrafish phenotype assays used for identifying potential hits. However, this may be target/assay dependent and thus requiring additional optimization steps to assess interference potential of tannins and chlorophylls before performing any screening assay.
Collapse
Affiliation(s)
| | - Mei Fong Ng
- Cancer Research Malaysia , Subang Jaya, Selangor, Malaysia
| | | | | | - Pei Jean Tan
- Cancer Research Malaysia , Subang Jaya, Selangor, Malaysia
| | - Vyomesh Patel
- Cancer Research Malaysia , Subang Jaya, Selangor, Malaysia
| |
Collapse
|
4
|
Velando A, Costa MM, Kim SY. Sex-specific phenotypes and metabolism-related gene expression in juvenile sticklebacks. Behav Ecol 2017. [DOI: 10.1093/beheco/arx129] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Alberto Velando
- Departamento de Ecoloxía e Bioloxía Animal, Campus As Lagoas, Universidade de Vigo, 36310 Vigo, Spain
| | - María M Costa
- Departamento de Ecoloxía e Bioloxía Animal, Campus As Lagoas, Universidade de Vigo, 36310 Vigo, Spain
| | - Sin-Yeon Kim
- Departamento de Ecoloxía e Bioloxía Animal, Campus As Lagoas, Universidade de Vigo, 36310 Vigo, Spain
| |
Collapse
|
5
|
Isolation and Characterization of Isofraxidin 7- O-(6'- O- p-Coumaroyl)- β-glucopyranoside from Artemisia capillaris Thunberg: A Novel, Nontoxic Hyperpigmentation Agent That Is Effective In Vivo. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017. [PMID: 28626485 PMCID: PMC5463131 DOI: 10.1155/2017/1401279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abnormalities in skin pigmentation can produce disorders such as albinism or melasma. There is a research need to discover novel compounds that safely and effectively regulate pigmentation. To identify novel modulators of pigmentation, we attempted to purify compounds from a bioactive fraction of the Korean medicinal plant Artemisia capillaris Thunberg. The novel compound isofraxidin 7-O-(6′-O-p-coumaroyl)-β-glucopyranoside (compound 1) was isolated and its pigmentation activity was characterized in mammalian melanocytes. Compound 1 stimulated melanin accumulation and increased tyrosinase activity, which regulates melanin synthesis. Moreover, compound 1 increased the expression of tyrosinase and the key melanogenesis regulator microphthalmia-associated transcription factor (MITF) in melanocytes. Compared to the parent compound, isofraxidin, compound 1 produced greater effects on these pigmentation parameters. To validate compound 1 as a novel hyperpigmentation agent in vivo, we utilized the zebrafish vertebrate model. Zebrafish treated with compound 1 showed higher melanogenesis and increased tyrosinase activity. Compound 1 treated embryos had no developmental defects and displayed normal cardiac function, indicating that this compound enhanced pigmentation without producing toxicity. In summary, our results describe the characterization of novel natural product compound 1 and its bioactivity as a pigmentation enhancer, demonstrating its potential as a therapeutic to treat hypopigmentation disorders.
Collapse
|
6
|
Wiley DS, Redfield SE, Zon LI. Chemical screening in zebrafish for novel biological and therapeutic discovery. Methods Cell Biol 2016; 138:651-679. [PMID: 28129862 DOI: 10.1016/bs.mcb.2016.10.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Zebrafish chemical screening allows for an in vivo assessment of small molecule modulation of biological processes. Compound toxicities, chemical alterations by metabolism, pharmacokinetic and pharmacodynamic properties, and modulation of cell niches can be studied with this method. Furthermore, zebrafish screening is straightforward and cost effective. Zebrafish provide an invaluable platform for novel therapeutic discovery through chemical screening.
Collapse
Affiliation(s)
- D S Wiley
- Stem Cell Program and Division of Hematology and Oncology, Childrens' Hospital Boston, Dana-Farber Cancer Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, United States
| | - S E Redfield
- Stem Cell Program and Division of Hematology and Oncology, Childrens' Hospital Boston, Dana-Farber Cancer Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, United States
| | - L I Zon
- Stem Cell Program and Division of Hematology and Oncology, Childrens' Hospital Boston, Dana-Farber Cancer Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, United States
| |
Collapse
|
7
|
|
8
|
Tabassum N, Tai H, Jung DW, Williams DR. Fishing for Nature's Hits: Establishment of the Zebrafish as a Model for Screening Antidiabetic Natural Products. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2015; 2015:287847. [PMID: 26681965 PMCID: PMC4670909 DOI: 10.1155/2015/287847] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/28/2015] [Indexed: 12/14/2022]
Abstract
Diabetes mellitus affects millions of people worldwide and significantly impacts their quality of life. Moreover, life threatening diseases, such as myocardial infarction, blindness, and renal disorders, increase the morbidity rate associated with diabetes. Various natural products from medicinal plants have shown potential as antidiabetes agents in cell-based screening systems. However, many of these potential "hits" fail in mammalian tests, due to issues such as poor pharmacokinetics and/or toxic side effects. To address this problem, the zebrafish (Danio rerio) model has been developed as a "bridge" to provide an experimentally convenient animal-based screening system to identify drug candidates that are active in vivo. In this review, we discuss the application of zebrafish to drug screening technologies for diabetes research. Specifically, the discovery of natural product-based antidiabetes compounds using zebrafish will be described. For example, it has recently been demonstrated that antidiabetic natural compounds can be identified in zebrafish using activity guided fractionation of crude plant extracts. Moreover, the development of fluorescent-tagged glucose bioprobes has allowed the screening of natural product-based modulators of glucose homeostasis in zebrafish. We hope that the discussion of these advances will illustrate the value and simplicity of establishing zebrafish-based assays for antidiabetic compounds in natural products-based laboratories.
Collapse
Affiliation(s)
- Nadia Tabassum
- New Drug Targets Laboratory, School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Hongmei Tai
- Department of Endocrinology, Yanji Hospital, Jilin 133000, China
| | - Da-Woon Jung
- New Drug Targets Laboratory, School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Darren R. Williams
- New Drug Targets Laboratory, School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| |
Collapse
|
9
|
Zheng W, Li G, Li X. Affinity purification in target identification: the specificity challenge. Arch Pharm Res 2015; 38:1661-85. [DOI: 10.1007/s12272-015-0635-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/07/2015] [Indexed: 12/16/2022]
|
10
|
Su D, Teoh CL, Kang NY, Yu X, Sahu S, Chang YT. Synthesis and systematic evaluation of dark resonance energy transfer (DRET)-based library and its application in cell imaging. Chem Asian J 2014; 10:581-5. [PMID: 25530300 DOI: 10.1002/asia.201403257] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 12/22/2022]
Abstract
In this paper, we report a new strategy for constructing a dye library with large Stokes shifts. By coupling a dark donor with BODIPY acceptors of tunable high quantum yield, a novel dark resonance energy transfer (DRET)-based library, named BNM, has been synthesized. Upon excitation of the dark donor (BDN) at 490 nm, the absorbed energy is transferred to the acceptor (BDM) with high efficiency, which was tunable in a broad range from 557 nm to 716 nm, with a high quantum yield of up to 0.8. It is noteworthy to mention that the majority of the non-radiative energy loss of the donor was converted into the acceptor's fluorescence output with a minimum leak of donor emission. Fluorescence imaging tested in live cells showed that the BNM compounds are cell-permeable and can also be employed for live-cell imaging. This is a new library which can be excited through a dark donor allowing for strong fluorescence emission in a wide range of wavelengths. Thus, the BNM library is well suited for high-throughput screening or multiplex experiments in biological applications by using a single laser excitation source.
Collapse
Affiliation(s)
- Dongdong Su
- Department of Chemistry & MedChem Program of Life Sciences, Institute National University of Singapore, 117543, Singapore (Singapore), Fax: (+65) 6779-1691; Singapore Bioimaging Consortium, Agency for Science Technology and Research (A*STAR), 138667, Singapore (Singapore)
| | | | | | | | | | | |
Collapse
|
11
|
Rennekamp AJ, Peterson RT. 15 years of zebrafish chemical screening. Curr Opin Chem Biol 2014; 24:58-70. [PMID: 25461724 DOI: 10.1016/j.cbpa.2014.10.025] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 12/13/2022]
Abstract
In 2000, the first chemical screen using living zebrafish in a multi-well plate was reported. Since then, more than 60 additional screens have been published describing whole-organism drug and pathway discovery projects in zebrafish. To investigate the scope of the work reported in the last 14 years and to identify trends in the field, we analyzed the discovery strategies of 64 primary research articles from the literature. We found that zebrafish screens have expanded beyond the use of developmental phenotypes to include behavioral, cardiac, metabolic, proliferative and regenerative endpoints. Additionally, many creative strategies have been used to uncover the mechanisms of action of new small molecules including chemical phenocopy, genetic phenocopy, mutant rescue, and spatial localization strategies.
Collapse
Affiliation(s)
- Andrew J Rennekamp
- Cardiovascular Research Center and Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA; Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Randall T Peterson
- Cardiovascular Research Center and Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA; Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.
| |
Collapse
|
12
|
Su D, Oh J, Lee SC, Lim JM, Sahu S, Yu X, Kim D, Chang YT. Dark to light! A new strategy for large Stokes shift dyes: coupling of a dark donor with tunable high quantum yield acceptors. Chem Sci 2014. [DOI: 10.1039/c4sc01821d] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
13
|
Lantz-McPeak S, Guo X, Cuevas E, Dumas M, Newport GD, Ali SF, Paule MG, Kanungo J. Developmental toxicity assay using high content screening of zebrafish embryos. J Appl Toxicol 2014; 35:261-72. [PMID: 24871937 DOI: 10.1002/jat.3029] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 04/18/2014] [Accepted: 04/18/2014] [Indexed: 01/06/2023]
Abstract
Typically, time-consuming standard toxicological assays using the zebrafish (Danio rerio) embryo model evaluate mortality and teratogenicity after exposure during the first 2 days post-fertilization. Here we describe an automated image-based high content screening (HCS) assay to identify the teratogenic/embryotoxic potential of compounds in zebrafish embryos in vivo. Automated image acquisition was performed using a high content microscope system. Further automated analysis of embryo length, as a statistically quantifiable endpoint of toxicity, was performed on images post-acquisition. The biological effects of ethanol, nicotine, ketamine, caffeine, dimethyl sulfoxide and temperature on zebrafish embryos were assessed. This automated developmental toxicity assay, based on a growth-retardation endpoint should be suitable for evaluating the effects of potential teratogens and developmental toxicants in a high throughput manner. This approach can significantly expedite the screening of potential teratogens and developmental toxicants, thereby improving the current risk assessment process by decreasing analysis time and required resources.
Collapse
Affiliation(s)
- Susan Lantz-McPeak
- Division of Neurotoxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Dinh TT, O'Leary M, Won SY, Li S, Arroyo L, Liu X, Defries A, Zheng B, Cutler SR, Chen X. Generation of a luciferase-based reporter for CHH and CG DNA methylation in Arabidopsis thaliana. SILENCE 2013; 4:1. [PMID: 23561294 PMCID: PMC3623655 DOI: 10.1186/1758-907x-4-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 03/20/2013] [Indexed: 12/24/2022]
Abstract
Background DNA methylation ensures genome integrity and regulates gene expression in diverse eukaryotes. In Arabidopsis, methylation occurs in three sequence contexts: CG, CHG and CHH. The initial establishment of DNA methylation at all three sequence contexts occurs through a process known as RNA-directed DNA methylation (RdDM), in which small RNAs bound by Argonaute4 (AGO4) guide DNA methylation at homologous loci through the de novo methyltransferase DRM2. Once established, DNA methylation at each of the three sequence contexts is maintained through different mechanisms. Although some players involved in RdDM and maintenance methylation have been identified, the underlying molecular mechanisms are not fully understood. To aid the comprehensive identification of players in DNA methylation, we generated a transgenic reporter system that permits genetic and chemical genetic screens in Arabidopsis. Results A dual 35S promoter (d35S) driven luciferase (LUC) reporter was introduced into Arabidopsis and LUCL, a line with a low basal level of luciferase activity, was obtained. LUCL was found to be a multi-copy, single-insertion transgene that contains methylated cytosines in CG, CHG and CHH contexts, with the highest methylation in the CG context. Methylation was present throughout the promoter and LUC coding region. Treatment with an inhibitor of cytosine methylation de-repressed luciferase activity. A mutation in MET1, which encodes the CG maintenance methyltransferase, drastically reduced CG methylation and de-repressed LUC expression. Mutations in AGO4 and DRM2 also de-repressed LUC expression, albeit to a smaller extent than loss of MET1. Using LUCL as a reporter line, we performed a chemical screen for compounds that de-repress LUC expression, and identified a chemical, methotrexate, known to be involved in biogenesis of the methyl donor. Conclusion We developed a luciferase-based reporter system, LUCL, which reports both RdDM and CG maintenance methylation in Arabidopsis. The low basal level of LUCL expression provides an easy readout in genetic and chemical genetic screens that will dissect the mechanisms of RdDM and methylation maintenance.
Collapse
Affiliation(s)
- Thanh Theresa Dinh
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Ziegler S, Pries V, Hedberg C, Waldmann H. Identifizierung der Zielproteine bioaktiver Verbindungen: Die Suche nach der Nadel im Heuhaufen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
16
|
Ziegler S, Pries V, Hedberg C, Waldmann H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 2013; 52:2744-92. [PMID: 23418026 DOI: 10.1002/anie.201208749] [Citation(s) in RCA: 356] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/10/2023]
Abstract
Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.
Collapse
Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | | | | | | |
Collapse
|
17
|
Jung DW, Williams DR. Reawakening atlas: chemical approaches to repair or replace dysfunctional musculature. ACS Chem Biol 2012; 7:1773-90. [PMID: 23043623 DOI: 10.1021/cb3003368] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Muscle diseases are major health concerns. For example, ischemic heart disease is the third most common cause of death. Cell therapy is an attractive approach for treating muscle diseases, although this is hampered by the need to generate large numbers of functional muscle cells. Small molecules have become established as attractive tools for modulating cell behavior and, in this review, we discuss the recent, rapid research advances made in the development of small molecule methods to facilitate the production of functional cardiac, skeletal, and smooth muscle cells. We also describe how new developments in small molecule strategies for muscle disease aim to induce repair and remodelling of the damaged tissues in situ. Recent progress has been made in developing small molecule cocktails that induce skeletal muscle regeneration, and these are discussed in a broader context, because a similar phenomenon occurs in the early stages of salamander appendage regeneration. Although formidable technical hurdles still remain, these new advances in small molecule-based methodologies should provide hope that cell therapies for patients suffering from muscle disease can be developed in the near future.
Collapse
Affiliation(s)
- Da-Woon Jung
- New Drug Targets Laboratory, School of Life Sciences, Gwangju Institute of Science and Technology, 1 Oryong-Dong,
Buk-Gu, Gwangju 500-712, Republic of Korea
| | - Darren R. Williams
- New Drug Targets Laboratory, School of Life Sciences, Gwangju Institute of Science and Technology, 1 Oryong-Dong,
Buk-Gu, Gwangju 500-712, Republic of Korea
| |
Collapse
|
18
|
Colanesi S, Taylor KL, Temperley ND, Lundegaard PR, Liu D, North TE, Ishizaki H, Kelsh RN, Patton EE. Small molecule screening identifies targetable zebrafish pigmentation pathways. Pigment Cell Melanoma Res 2012; 25:131-43. [PMID: 22252091 DOI: 10.1111/j.1755-148x.2012.00977.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Small molecules complement genetic mutants and can be used to probe pigment cell biology by inhibiting specific proteins or pathways. Here, we present the results of a screen of active compounds for those that affect the processes of melanocyte and iridophore development in zebrafish and investigate the effects of a few of these compounds in further detail. We identified and confirmed 57 compounds that altered pigment cell patterning, number, survival, or differentiation. Additional tissue targets and toxicity of small molecules are also discussed. Given that the majority of cell types, including pigment cells, are conserved between zebrafish and other vertebrates, we present these chemicals as molecular tools to study developmental processes of pigment cells in living animals and emphasize the value of zebrafish as an in vivo system for testing the on- and off-target activities of clinically active drugs.
Collapse
Affiliation(s)
- Sarah Colanesi
- Developmental Biology Programme, Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
As the current paradigms of drug discovery evolve, it has become clear that a more comprehensive understanding of the interactions between small molecules and organismal biology will be vital. The zebrafish is emerging as a complement to existing in vitro technologies and established preclinical in vivo models that can be scaled for high-throughput. In this review, we highlight the current status of zebrafish toxicology studies, identify potential future niches for the model in the drug development pipeline, and define the hurdles that must be overcome as zebrafish technologies are refined for systematic toxicology.
Collapse
Affiliation(s)
- Randall T Peterson
- Harvard Medical School, Massachusetts General Hospital, and Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
20
|
In vivo imaging and quantitative analysis of changes in axon length using transgenic zebrafish embryos. Neurotoxicol Teratol 2011; 33:618-23. [PMID: 21903162 DOI: 10.1016/j.ntt.2011.08.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 08/23/2011] [Accepted: 08/24/2011] [Indexed: 11/22/2022]
Abstract
We describe an imaging procedure to measure axon length in zebrafish embryos in vivo. Automated fluorescent image acquisition was performed with the ImageXpress Micro high content screening reader and further analysis of axon lengths was performed on archived images using AcuityXpress software. We utilized the Neurite Outgrowth Application module with a customized protocol (journal) to measure the axons. Since higher doses of ethanol (2-2.5%, v/v) have been shown to deform motor neurons and axons during development, here we used ethanol to treat transgenic [hb9:GFP (green fluorescent protein)] zebrafish embryos at 28 hpf (hours post-fertilization). These embryos express GFP in the motor neurons and their axons. Embryos after ethanol treatment were arrayed in 384-well plates for automated fluorescent image acquisition in vivo. Average axon lengths of high dose ethanol-treated embryos were significantly lower than the control. Another experiment showed that there was no significant difference in the axon lengths between the embryos grown for 24h at 22°C and 28.5°C. These test experiments demonstrate that using axon development as an end-point, compound screening can be performed in a time-efficient manner.
Collapse
|
21
|
Tan JL, Zon LI. Chemical screening in zebrafish for novel biological and therapeutic discovery. Methods Cell Biol 2011; 105:493-516. [PMID: 21951544 DOI: 10.1016/b978-0-12-381320-6.00021-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Zebrafish chemical screening allows for an in vivo assessment of small molecule modulation of biological processes. Compound toxicities, chemical alterations by metabolism, pharmacokinetic and pharmacodynamic properties, and modulation of cell niches can be studied with this method. Furthermore, zebrafish screening is straightforward and cost-effective. Zebrafish provide an invaluable platform for novel therapeutic discovery through chemical screening.
Collapse
Affiliation(s)
- Justin L Tan
- Stem Cell Program and Division of Hematology and Oncology, Children’s Hospital Boston, Dana-Farber Cancer Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, Massachusetts, USA
| | | |
Collapse
|
22
|
Abstract
The zebrafish is proving to be highly amenable to in vivo small molecule screening. With a growing number of screens successfully completed, a rich interface is being created between disciplines that have historically used zebrafish (e.g., embryology and genetics) and disciplines focused on small molecules (e.g., chemistry and pharmacology). Navigating this interface requires consideration of the unique demands of conducting high-throughput screening in vivo. In this chapter, we discuss design elements of successful zebrafish screens, established screening methods, and approaches for mechanism of action studies following discovery of novel small molecules. These methods are enabling the zebrafish to have an increasingly positive impact on biomedical research and drug development.
Collapse
Affiliation(s)
- Randall T Peterson
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | | |
Collapse
|
23
|
|
24
|
Taylor KL, Grant NJ, Temperley ND, Patton EE. Small molecule screening in zebrafish: an in vivo approach to identifying new chemical tools and drug leads. Cell Commun Signal 2010; 8:11. [PMID: 20540792 PMCID: PMC2912314 DOI: 10.1186/1478-811x-8-11] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 06/12/2010] [Indexed: 12/19/2022] Open
Abstract
In the past two decades, zebrafish genetic screens have identified a wealth of mutations that have been essential to the understanding of development and disease biology. More recently, chemical screens in zebrafish have identified small molecules that can modulate specific developmental and behavioural processes. Zebrafish are a unique vertebrate system in which to study chemical genetic systems, identify drug leads, and explore new applications for known drugs. Here, we discuss some of the advantages of using zebrafish in chemical biology, and describe some important and creative examples of small molecule screening, drug discovery and target identification.
Collapse
Affiliation(s)
- Kerrie L Taylor
- MRC Human Genetics Unit and the Division of Cancer Research, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, UK.
| | | | | | | |
Collapse
|
25
|
Zebrafish beta-adrenergic receptor mRNA expression and control of pigmentation. Gene 2009; 446:18-27. [PMID: 19540320 DOI: 10.1016/j.gene.2009.06.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 06/12/2009] [Accepted: 06/15/2009] [Indexed: 01/08/2023]
Abstract
Beta adrenergic receptors (beta-ARs) are members of the G-protein-coupled receptor superfamily and mediate various physiological processes in many species. The expression patterns and functions of beta-ARs in zebrafish are, however, largely unknown. We have identified zebrafish beta-AR orthologs, which we have designated as adrb1, adrb2a, adrb2b, adrb3a and adrb3b. adrb1 was found to be expressed in the heart and brain. Expression of adrb2a predominated in the brain and skin, whereas adrb2b was found to be highly expressed in muscle, pancreas and liver. Both adrb3a and adrb3b were exclusively expressed in blood. Knock-down of these beta-ARs by morpholino oligonucleotides revealed a functional importance of adrb2a in pigmentation. Expression of atp5a1 and atp5b, genes that encode subunits of F1F0-ATPase, which is known to be involved in pigmentation, was significantly increased by knock-down of adrb2a. Our data suggest that adrb2a may regulate pigmentation, partly by modulating F1F0-ATPase.
Collapse
|
26
|
Wheeler GN, Brändli AW. Simple vertebrate models for chemical genetics and drug discovery screens: Lessons from zebrafish andXenopus. Dev Dyn 2009; 238:1287-308. [DOI: 10.1002/dvdy.21967] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
|
27
|
Tomlinson ML, Guan P, Morris RJ, Fidock MD, Rejzek M, Garcia-Morales C, Field RA, Wheeler GN. A chemical genomic approach identifies matrix metalloproteinases as playing an essential and specific role in Xenopus melanophore migration. ACTA ACUST UNITED AC 2009; 16:93-104. [PMID: 19171309 DOI: 10.1016/j.chembiol.2008.12.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 12/10/2008] [Accepted: 12/12/2008] [Indexed: 01/27/2023]
Abstract
To dissect the function of matrix metalloproteinases (MMPs) involved in cellular migration in vivo, we undertook both a forward chemical genomic screen and a functional approach to discover modulators of melanophore (pigment cell) migration in Xenopus laevis. We identified the 8-quinolinol derivative NSC 84093 as affecting melanophore migration in the developing embryo and have shown it to act as a MMP inhibitor. Potential targets of NSC 84093 investigated include MMP-14 and MMP-2. MMP-14 is expressed in migrating neural crest cells from which melanophores are derived. MMP-2 is expressed at the relevant time of development and in a pattern that suggests it contributes to melanophore migration. Morpholino-mediated knockdown of both MMPs demonstrates they play a key role in melanophore migration and partially phenocopy the effect of NSC 84093.
Collapse
|
28
|
Richardson J, Lundegaard PR, Reynolds NL, Dorin JR, Porteous DJ, Jackson IJ, Patton EE. mc1r Pathway regulation of zebrafish melanosome dispersion. Zebrafish 2009; 5:289-95. [PMID: 19133827 DOI: 10.1089/zeb.2008.0541] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Zebrafish rapidly alter their pigmentation in response to environmental changes. For black melanocytes, this change is due to aggregation or dispersion of melanin in the cell. Dispersion and aggregation are controlled by intracellular cyclic adenosine monophosphate (cAMP) levels, which increase upon stimulation by alpha melanocyte-stimulating hormone (alpha-MSH) or reduce with melanin-concentrating hormone (MCH). In mammals and birds, the melanocortin-1-receptor (MC1R) responds to MSH, and stimulates the synthesis of black eumelanin. While MSH-cAMP signaling stimulates melanogenesis in mammals, and melanosome dispersal in cold-blood vertebrates, the pathway components are highly conserved. However, it has only been assumed that mc1r mediates melanosome dispersal in fish. Here, using morpholino oligonucleotides designed to knockdown mc1r expression, we find that mc1r morphants are unable to disperse melanosomes when grown in dark conditions. We also use chemical modifiers of the cAMP pathway, and find an unexpected response to the specific phosphodiesterase 4 (PDE4) inhibitor, rolipram, in melanosome dispersal. When treated with the drug, melanosomes fail to fully disperse in dark conditions, despite presumed increased levels of cAMP, and in contrast to the effects of the nonselective PDE inhibitor, 3-isobutyl-1-methylxanthine. In conclusion, we demonstrate a direct role for mc1r in zebrafish melanosome dispersal in response to background, and use chemical modification of this pathway to uncover a possible new layer of regulation in melanosome dispersal in zebrafish.
Collapse
Affiliation(s)
- Jennifer Richardson
- Institute for Genetics & Molecular Medicine , MRC Human Genetics Unit and The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
29
|
Robert S, Raikhel NV, Hicks GR. Powerful partners: Arabidopsis and chemical genomics. THE ARABIDOPSIS BOOK 2009; 7:e0109. [PMID: 22303245 PMCID: PMC3243329 DOI: 10.1199/tab.0109] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Chemical genomics (i.e. genomics scale chemical genetics) approaches capitalize on the ability of low molecular mass molecules to modify biological processes. Such molecules are used to modify the activity of a protein or a pathway in a manner that it is tunable and reversible. Bioactive chemicals resulting from forward or reverse chemical screens can be useful in understanding and dissecting complex biological processes due to the essentially limitless variation in structure and activities inherent in chemical space. A major advantage of this approach as a powerful addition to conventional plant genetics is the fact that chemical genomics can address loss-of-function lethality and redundancy. Furthermore, the ability of chemicals to be added at will and to act quickly can permit the study of processes that are highly dynamic such as endomembrane trafficking. An important aspect of utilizing small molecules effectively is to characterize bioactive chemicals in detail including an understanding of structure-activity relationships and the identification of active and inactive analogs. Bioactive chemicals can be useful as reagents to probe biological pathways directly. However, the identification of cognate targets and their pathways is also informative and can be achieved by screens for genetic resistance or hypersensitivity in Arabidopsis thaliana or other organisms from which the results can be translated to plants. In addition, there are approaches utilizing "tagged" chemical libraries that possess reactive moieties permitting the immobilization of active compounds. This opens the possibility for biochemical purification of putative cognate targets. We will review approaches to screen for bioactive chemicals that affect biological processes in Arabidopsis and provide several examples of the power and challenges inherent in this new approach in plant biology.
Collapse
Affiliation(s)
- Stéphanie Robert
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
- Current address: VIB Department of Plant Systems Biology, University of Ghent, 9052 Ghent, Belgium
| | - Natasha V. Raikhel
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Glenn R. Hicks
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
- Address correspondence to
| |
Collapse
|
30
|
Leslie BJ, Hergenrother PJ. Identification of the cellular targets of bioactive small organic molecules using affinity reagents. Chem Soc Rev 2008; 37:1347-60. [PMID: 18568161 DOI: 10.1039/b702942j] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The elucidation of molecular targets of bioactive small organic molecules remains a significant challenge in modern biomedical research and drug discovery. This tutorial review summarizes strategies for the derivatization of bioactive small molecules and their use as affinity probes to identify cellular binding partners. Special emphasis is placed on logistical concerns as well as common problems encountered during such target identification experiments. The roadmap provided is a guide through the process of affinity probe selection, target identification, and downstream target validation.
Collapse
Affiliation(s)
- Benjamin J Leslie
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | | |
Collapse
|
31
|
Ni-Komatsu L, Orlow SJ. Chemical genetic screening identifies tricyclic compounds that decrease cellular melanin content. J Invest Dermatol 2008; 128:1236-47. [PMID: 18007583 DOI: 10.1038/sj.jid.5701163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A screen of a library of 2,000 drugs and natural products in murine melanocytes identified 10 tricyclic antidepressants (TCAs) as compounds that potently decreased intracellular melanin content. The rank order of potency of these compounds for decreasing melanin content was different than their relative potencies as antidepressants. These compounds had no effect on either the level or the enzymatic activity of cellular tyrosinase (Tyr). Increased presence of both Tyr and melanin in the culture media was observed in treated melanocytes. Immunofluorescence localization revealed that these compounds decreased intracellular melanin content by disrupting the intracellular trafficking of Tyr gene family proteins. In treated melanocytes, Tyr, Tyr-related protein 1, and dopachrome tautomerase accumulated in enlarged granules distributed throughout the cytoplasm. Colocalization of Tyr with lysosome-associated membrane protein 1 was observed within many of these granules. Partial colocalization of Tyr with the Hermansky-Pudlak syndrome 1 gene product observed in control melanocytes was abolished by TCA treatment. Our results show that these compounds decreased intracellular melanin content by altering the trafficking of Tyr gene family proteins and inducing abnormal secretion of Tyr. Results from our screening have implications for the design of products for skin lightening and treatment of hyperpigmentation.
Collapse
Affiliation(s)
- Li Ni-Komatsu
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, New York 10016, USA
| | | |
Collapse
|
32
|
Ni-Komatsu L, Orlow SJ. Identification of Novel Pigmentation Modulators by Chemical Genetic Screening. J Invest Dermatol 2007; 127:1585-92. [PMID: 17568802 DOI: 10.1038/sj.jid.5700852] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is a continual need for compounds that effectively modulate melanin synthesis. To identify novel pigmentation modulators and their cellular targets, chemical genetic screenings were performed with triazine-based combinatorial libraries that include various linkers as intrinsic components of the small molecules in the library. The linker provides a ready means of attachment to beads, eliminating several common time-consuming downstream steps in the isolation of cellular targets for the small molecules of interest. Twelve compounds were identified as novel pigmentation modulators from various screenings performed in normal and albino murine melanocytes and zebrafish. Target identification by affinity chromatography revealed unexpected roles for prohibitin and mitochondrial F1F0-adenotriphosphatase in the regulation of mammalian pigmentation. The identification of prohibitin, a "scaffold protein", as a propigmentation effector represents a novel mechanism by which propigmentary signals are transduced. Results from our screenings provide potential active agents and targets for the medical and aesthetic treatment of disorders of pigmentation.
Collapse
Affiliation(s)
- Li Ni-Komatsu
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, New York 10016, USA
| | | |
Collapse
|
33
|
Kim YK, Chang YT. Tagged library approach facilitates forward chemical genetics. MOLECULAR BIOSYSTEMS 2007; 3:392-7. [PMID: 17533452 DOI: 10.1039/b702321a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Forward chemical genetics has been highlighted as a new method for the study of various biological pathways using exogenous ligands. However, limited success in the field has demonstrated that, in many cases, it is not feasible to determine the protein targets of small-molecule probes. Identifying protein targets is an integral part of forward chemical genetics and is also the most challenging. Over the past decade, several biochemical and genetic methods have been developed to facilitate target identification processes. Even so, one of the major difficulties is that these methods require the chemical modification of active compounds, with a significant amount of structure-activity relationship (SAR) study to ensure that the small-molecule tags do not compromise bioactivity. In this article, we will highlight a new strategy for small molecule libraries that have built-in linkers in order to avoid this well-known problem and demonstrate their successful use in forward chemical genetics.
Collapse
Affiliation(s)
- Yun Kyung Kim
- Department of Chemistry, New York University, New York, NY 10003, USA
| | | |
Collapse
|
34
|
Rosania GR, Crippen G, Woolf P, States D, Shedden K. A Cheminformatic Toolkit for Mining Biomedical Knowledge. Pharm Res 2007; 24:1791-802. [PMID: 17385012 DOI: 10.1007/s11095-007-9285-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Accepted: 02/27/2007] [Indexed: 01/31/2023]
Abstract
PURPOSE Cheminformatics can be broadly defined to encompass any activity related to the application of information technology to the study of properties, effects and uses of chemical agents. One of the most important current challenges in cheminformatics is to allow researchers to search databases of biomedical knowledge, using chemical structures as input. MATERIALS AND METHODS An important step towards this goal was the establishment of PubChem, an open, centralized database of small molecules accessible through the World Wide Web. While PubChem is primarily intended to serve as a repository for high throughput screening data from federally-funded screening centers and academic research laboratories, the major impact of PubChem could also reside in its ability to serve as a chemical gateway to biomedical databases such as PubMed. CONCLUSION This article will review cheminformatic tools that can be applied to facilitate annotation of PubChem through links to the scientific literature; to integrate PubChem with transcriptomic, proteomic, and metabolomic datasets; to incorporate results of numerical simulations of physiological systems into PubChem annotation; and ultimately, to translate data of chemical genomics screening efforts into information that will benefit biomedical researchers and physician scientists across all therapeutic areas.
Collapse
Affiliation(s)
- Gus R Rosania
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, 428 Church Street, Ann Arbor, MI 48109, USA.
| | | | | | | | | |
Collapse
|
35
|
Chang YT. Small-molecule switch for zebrafish gene expression. Nat Chem Biol 2007; 3:135-6. [PMID: 17301797 DOI: 10.1038/nchembio0307-135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
36
|
Tomlinson ML, Field RA, Wheeler GN. Xenopus as a model organism in developmental chemical genetic screens. MOLECULAR BIOSYSTEMS 2005; 1:223-8. [PMID: 16880986 DOI: 10.1039/b506103b] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical genetics is a potentially powerful tool for studying developmental processes in vertebrate systems. We present data showing Xenopus laevis as a model organism in which systematic chemical genetic screens can be carried out. Previous forward chemical genetic screens, including those with developing zebrafish embryos, have demonstrated the nature and value of biological information gained with this approach. We show how amenable Xenopus is to chemical genetics by investigating a series of compounds either with known biochemical effects, or previously identified to give developmental phenotypes, on a range of biological functions, including the development of pigmentation, the heart and the central nervous system in zebrafish. We have found that the compounds give comparable phenotypes when applied to developing Xenopus embryos. We have also studied the penetrance and expressivity of these chemical genetic phenotypes in relation to genetic variation and the developmental window during which the compound is present. Finally, we assess the feasibility and the potential throughput of a screen in this vertebrate species.
Collapse
|