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Williams JD, Pu F, Sawicki JW, Elsen NL. Ultra-high-throughput mass spectrometry in drug discovery: fundamentals and recent advances. Expert Opin Drug Discov 2024; 19:291-301. [PMID: 38111363 DOI: 10.1080/17460441.2023.2293153] [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: 10/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
INTRODUCTION Ultra-high-throughput mass spectrometry, uHT-MS, is a technology that utilizes ionization and sample delivery technologies optimized to enable sampling from well plates at > 1 sample per second. These technologies do not need a chromatographic separation step and can be utilized in a wide variety of assays to detect a broad range of analytes including small molecules, lipids, and proteins. AREAS COVERED This manuscript provides a brief historical review of high-throughput mass spectrometry and the recently developed technologies that have enabled uHT-MS. The report also provides examples and references on how uHT-MS has been used in biochemical and chemical assays, nuisance compound profiling, protein analysis and high throughput experimentation for chemical synthesis. EXPERT OPINION The fast analysis time provided by uHT-MS is transforming how biochemical and chemical assays are performed in drug discovery. The potential to associate phenotypic responses produced by 1000's of compound treatments with changes in endogenous metabolite and lipid signals is becoming feasible. With the augmentation of simple, fast, high-throughput sample preparation, the scope of uHT-MS usage will increase. However, it likely will not supplant LC-MS for analyses that require low detection limits from complex matrices or characterization of complex biotherapeutics such as antibody-drug conjugates.
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Affiliation(s)
| | - Fan Pu
- Abbvie Discovery Research, North Chicago, IL, USA
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2
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Izquierdo M, Lin D, O'Neill S, Webster LA, Paterson C, Thomas J, Aguado ME, Colina Araújo E, Alpízar-Pedraza D, Joji H, MacLean L, Hope A, Gray DW, Zoltner M, Field MC, González-Bacerio J, De Rycker M. Identification of a potent and selective LAPTc inhibitor by RapidFire-Mass Spectrometry, with antichagasic activity. PLoS Negl Trop Dis 2024; 18:e0011956. [PMID: 38359089 PMCID: PMC10901353 DOI: 10.1371/journal.pntd.0011956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 02/28/2024] [Accepted: 01/31/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Chagas disease is caused by the protozoan parasite Trypanosoma cruzi and leads to ~10,000 deaths each year. Nifurtimox and benznidazole are the only two drugs available but have significant adverse effects and limited efficacy. New chemotherapeutic agents are urgently required. Here we identified inhibitors of the acidic M17 leucyl-aminopeptidase from T. cruzi (LAPTc) that show promise as novel starting points for Chagas disease drug discovery. METHODOLOGY/PRINCIPAL FINDINGS A RapidFire-MS screen with a protease-focused compound library identified novel LAPTc inhibitors. Twenty-eight hits were progressed to the dose-response studies, from which 12 molecules inhibited LAPTc with IC50 < 34 μM. Of these, compound 4 was the most potent hit and mode of inhibition studies indicate that compound 4 is a competitive LAPTc inhibitor, with Ki 0.27 μM. Compound 4 is selective with respect to human LAP3, showing a selectivity index of >500. Compound 4 exhibited sub-micromolar activity against intracellular T. cruzi amastigotes, and while the selectivity-window against the host cells was narrow, no toxicity was observed for un-infected HepG2 cells. In silico modelling of the LAPTc-compound 4 interaction is consistent with the competitive mode of inhibition. Molecular dynamics simulations reproduce the experimental binding strength (-8.95 kcal/mol), and indicate a binding mode based mainly on hydrophobic interactions with active site residues without metal cation coordination. CONCLUSIONS/SIGNIFICANCE Our data indicates that these new LAPTc inhibitors should be considered for further development as antiparasitic agents for the treatment of Chagas disease.
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Affiliation(s)
- Maikel Izquierdo
- Centre for Protein Studies, Faculty of Biology, University of Havana, La Habana, Cuba
| | - De Lin
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Sandra O'Neill
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Lauren A Webster
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Christy Paterson
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - John Thomas
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Mirtha Elisa Aguado
- Centre for Protein Studies, Faculty of Biology, University of Havana, La Habana, Cuba
| | - Enrique Colina Araújo
- Department of Biochemistry, Faculty of Biology, University of Havana, La Habana, Cuba
| | | | - Halimatu Joji
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Lorna MacLean
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Anthony Hope
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - David W Gray
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Martin Zoltner
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| | - Jorge González-Bacerio
- Centre for Protein Studies, Faculty of Biology, University of Havana, La Habana, Cuba
- Department of Biochemistry, Faculty of Biology, University of Havana, La Habana, Cuba
| | - Manu De Rycker
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
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3
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Dueñas ME, Peltier‐Heap RE, Leveridge M, Annan RS, Büttner FH, Trost M. Advances in high-throughput mass spectrometry in drug discovery. EMBO Mol Med 2022; 15:e14850. [PMID: 36515561 PMCID: PMC9832828 DOI: 10.15252/emmm.202114850] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 12/15/2022] Open
Abstract
High-throughput (HT) screening drug discovery, during which thousands or millions of compounds are screened, remains the key methodology for identifying active chemical matter in early drug discovery pipelines. Recent technological developments in mass spectrometry (MS) and automation have revolutionized the application of MS for use in HT screens. These methods allow the targeting of unlabelled biomolecules in HT assays, thereby expanding the breadth of targets for which HT assays can be developed compared to traditional approaches. Moreover, these label-free MS assays are often cheaper, faster, and more physiologically relevant than competing assay technologies. In this review, we will describe current MS techniques used in drug discovery and explain their advantages and disadvantages. We will highlight the power of mass spectrometry in label-free in vitro assays, and its application for setting up multiplexed cellular phenotypic assays, providing an exciting new tool for screening compounds in cell lines, and even primary cells. Finally, we will give an outlook on how technological advances will increase the future use and the capabilities of mass spectrometry in drug discovery.
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Affiliation(s)
- Maria Emilia Dueñas
- Laboratory for Biomedical Mass Spectrometry, Biosciences InstituteNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Rachel E Peltier‐Heap
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Melanie Leveridge
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Roland S Annan
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Frank H Büttner
- Drug Discovery Sciences, High Throughput BiologyBoehringer Ingelheim Pharma GmbH&CoKGBiberachGermany
| | - Matthias Trost
- Laboratory for Biomedical Mass Spectrometry, Biosciences InstituteNewcastle UniversityNewcastle‐upon‐TyneUK
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4
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Tao D, Xu M, Farkhondeh A, Burns AP, Rodems S, Might M, Zheng W, LeClair CA. High-throughput protein modification quantitation analysis using intact protein MRM and its application on hENGase inhibitor screening. Talanta 2021; 231:122384. [PMID: 33965046 DOI: 10.1016/j.talanta.2021.122384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022]
Abstract
Proteins are widely used as drug targets, enzyme substrates, and biomarkers for numerous diseases. The emerging demand for proteins quantitation has been increasing in multiple fields. Currently, there is still a big gap for high-throughput protein quantitation at intact protein level using label-free method. Here we choose ribonuclease B (RNB) as a model, which is the substrate for human endo-β-N-acetylglucosaminidase (hENGase), a promising drug target for the treatment of N-Glycanase deficiency. Intact proteinlevel multiple reaction monitoring (MRM) methods were initally developed and optimized to quantify RNB and deglycosylated RNB (RNB-deg), with the S/N ratio improved by nearly 20-fold compared to the traditional full MS scan methods. To further increase the throughput making it possible for hENGase inhibitors screen, the protein MRM methods were introduced to the RapidFire-MS/MS system, achieving at least 12-fold throughput improvement. This assay was further optimized into 384-well plate format for compound screening with S/B ratio >37-fold and Z' factor >0.7 that is suitable for high-throughput screening of compound collections with a speed of 2 h per 384-well plate and an ability to screen over 3000 compounds per day at a single concentration dose. This 384-well plate based automated SPE-MS/MS assay is efficient and robust for compound screening and the assay format has a wide applicability to protein targets for other disease models.
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Affiliation(s)
- Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA.
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Atena Farkhondeh
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Andrew P Burns
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | | | - Matthew Might
- University of Alabama at Birmingham, Birmingham, AL, 35210, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA.
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5
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McLaren DG, Shah V, Wisniewski T, Ghislain L, Liu C, Zhang H, Saldanha SA. High-Throughput Mass Spectrometry for Hit Identification: Current Landscape and Future Perspectives. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:168-191. [PMID: 33482074 DOI: 10.1177/2472555220980696] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
For nearly two decades mass spectrometry has been used as a label-free, direct-detection method for both functional and affinity-based screening of a wide range of therapeutically relevant target classes. Here, we present an overview of several established and emerging mass spectrometry platforms and summarize the unique strengths and performance characteristics of each as they apply to high-throughput screening. Multiple examples from the recent literature are highlighted in order to illustrate the power of each individual technique, with special emphasis given to cases where the use of mass spectrometry was found to be differentiating when compared with other detection formats. Indeed, as many of these examples will demonstrate, the inherent strengths of mass spectrometry-sensitivity, specificity, wide dynamic range, and amenability to complex matrices-can be leveraged to enhance the discriminating power and physiological relevance of assays included in screening cascades. It is our hope that this review will serve as a useful guide to readers of all backgrounds and experience levels on the applicability and benefits of mass spectrometry in the search for hits, leads, and, ultimately, drugs.
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6
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A direct peptide reactivity assay using a high-throughput mass spectrometry screening platform for detection of skin sensitizers. Toxicol Lett 2020; 338:67-77. [PMID: 33290830 DOI: 10.1016/j.toxlet.2020.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 11/23/2022]
Abstract
Chemical-peptide conjugation is the molecular initiating event in skin sensitization. The OECD test guideline uses a high-performance liquid chromatography/ultraviolet (HPLC/UV) detection method to quantify chemical-peptide conjugation in a direct peptide reactivity assay (DPRA), which measures the depletion of two synthetic peptides containing lysine or cysteine residues. To improve assay throughput, sensitivity and accuracy, an automated 384-well plate-based RapidFire solid-phase extraction (SPE) system coupled with tandem mass spectrometry (MS/MS) DPRA was developed and validated in the presence of a newly designed internal standard. Compared to the HPLC/UV-based DPRA, the automated SPE-MS/MS-based DPRA improved throughput from 16 min to 10 s per sample, and substrate peptides usage was reduced from 100 mM to 5 μM. When implementing the SPE-MS/MS-based DPRA into a high-throughput platform, we found 10 compounds that depleted lysine peptide and 24 compounds that depleted cysteine peptide (including 7 unreported chemicals from 55 compounds we tested) in a concentration-response manner. The adduct formation between cysteine and cinnamic aldehyde and ethylene glycol dimethacrylate were further analyzed using high-performance liquid chromatography time-of-flight mass spectrometry (HPLC-TOF-MS) to confirm the conjugation. Overall, the automated SPE-MS/MS-based platform is an efficient, economic, and accurate way to detect skin sensitizers.
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7
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Clausse V, Tao D, Debnath S, Fang Y, Tagad HD, Wang Y, Sun H, LeClair CA, Mazur SJ, Lane K, Shi ZD, Vasalatiy O, Eells R, Baker LK, Henderson MJ, Webb MR, Shen M, Hall MD, Appella E, Appella DH, Coussens NP. Physiologically relevant orthogonal assays for the discovery of small-molecule modulators of WIP1 phosphatase in high-throughput screens. J Biol Chem 2019; 294:17654-17668. [PMID: 31481464 PMCID: PMC6873202 DOI: 10.1074/jbc.ra119.010201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Indexed: 01/07/2023] Open
Abstract
WT P53-Induced Phosphatase 1 (WIP1) is a member of the magnesium-dependent serine/threonine protein phosphatase (PPM) family and is induced by P53 in response to DNA damage. In several human cancers, the WIP1 protein is overexpressed, which is generally associated with a worse prognosis. Although WIP1 is an attractive therapeutic target, no potent, selective, and bioactive small-molecule modulator with favorable pharmacokinetics has been reported. Phosphatase enzymes are among the most challenging targets for small molecules because of the difficulty of achieving both modulator selectivity and bioavailability. Another major obstacle has been the availability of robust and physiologically relevant phosphatase assays that are suitable for high-throughput screening. Here, we describe orthogonal biochemical WIP1 activity assays that utilize phosphopeptides from native WIP1 substrates. We optimized an MS assay to quantify the enzymatically dephosphorylated peptide reaction product in a 384-well format. Additionally, a red-shifted fluorescence assay was optimized in a 1,536-well format to enable real-time WIP1 activity measurements through the detection of the orthogonal reaction product, Pi. We validated these two optimized assays by quantitative high-throughput screening against the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection and used secondary assays to confirm and evaluate inhibitors identified in the primary screen. Five inhibitors were further tested with an orthogonal WIP1 activity assay and surface plasmon resonance binding studies. Our results validate the application of miniaturized physiologically relevant and orthogonal WIP1 activity assays to discover small-molecule modulators from high-throughput screens.
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Affiliation(s)
- Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Subrata Debnath
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Harichandra D Tagad
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Hongmao Sun
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Kelly Lane
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Zhen-Dan Shi
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Olga Vasalatiy
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Rebecca Eells
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Lynn K Baker
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Martin R Webb
- Francis Crick Institute, 1 Midland Road, London NW1 AT, United Kingdom
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Ettore Appella
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
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8
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Kempa EE, Hollywood KA, Smith CA, Barran PE. High throughput screening of complex biological samples with mass spectrometry – from bulk measurements to single cell analysis. Analyst 2019; 144:872-891. [DOI: 10.1039/c8an01448e] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We review the state of the art in HTS using mass spectrometry with minimal sample preparation from complex biological matrices. We focus on industrial and biotechnological applications.
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Affiliation(s)
- Emily E. Kempa
- Michael Barber Centre for Collaborative Mass Spectrometry
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
| | - Katherine A. Hollywood
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM)
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester M1 7DN
- UK
| | - Clive A. Smith
- Sphere Fluidics Limited
- The Jonas-Webb Building
- Babraham Research Campus
- Cambridge
- UK
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
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9
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Kharel Y, Agah S, Huang T, Mendelson AJ, Eletu OT, Barkey-Bircann P, Gesualdi J, Smith JS, Santos WL, Lynch KR. Saccharomyces cerevisiae as a platform for assessing sphingolipid lipid kinase inhibitors. PLoS One 2018; 13:e0192179. [PMID: 29672528 PMCID: PMC5908134 DOI: 10.1371/journal.pone.0192179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/17/2018] [Indexed: 12/05/2022] Open
Abstract
Successful medicinal chemistry campaigns to discover and optimize sphingosine kinase inhibitors require a robust assay for screening chemical libraries and for determining rank order potencies. Existing assays for these enzymes are laborious, expensive and/or low throughput. The toxicity of excessive levels of phosphorylated sphingoid bases for the budding yeast, Saccharomyces cerevisiae, affords an assay wherein inhibitors added to the culture media rescue growth in a dose-dependent fashion. Herein, we describe our adaptation of a simple, inexpensive, and high throughput assay for assessing inhibitors of sphingosine kinase types 1 and 2 as well as ceramide kinase and for testing enzymatic activity of sphingosine kinase type 2 mutants. The assay was validated using recombinant enzymes and generally agrees with the rank order of potencies of existing inhibitors.
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Affiliation(s)
- Yugesh Kharel
- Departments of Pharmacology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Sayeh Agah
- Departments of Pharmacology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Tao Huang
- Departments of Pharmacology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Anna J. Mendelson
- Departments of Pharmacology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Oluwafunmilayo T. Eletu
- Departments of Pharmacology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Peter Barkey-Bircann
- Departments of Pharmacology, University of Virginia, Charlottesville, Virginia, United States of America
| | - James Gesualdi
- Departments of Pharmacology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jeffrey S. Smith
- Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Webster L. Santos
- Department of Chemistry and VT Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Kevin R. Lynch
- Departments of Pharmacology, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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10
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Snider JM, Snider AJ, Obeid LM, Luberto C, Hannun YA. Probing de novo sphingolipid metabolism in mammalian cells utilizing mass spectrometry. J Lipid Res 2018; 59:1046-1057. [PMID: 29610123 DOI: 10.1194/jlr.d081646] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 03/26/2018] [Indexed: 12/24/2022] Open
Abstract
Sphingolipids constitute a dynamic metabolic network that interconnects several bioactive molecules, including ceramide (Cer), sphingosine (Sph), Sph 1-phosphate, and Cer 1-phosphate. The interconversion of these metabolites is controlled by a cohort of at least 40 enzymes, many of which respond to endogenous or exogenous stimuli. Typical probing of the sphingolipid pathway relies on sphingolipid mass levels or determination of the activity of individual enzymes. Either approach is unable to provide a complete analysis of flux through sphingolipid metabolism, which, given the interconnectivity of the sphingolipid pathway, is critical information to identify nodes of regulation. Here, we present a one-step in situ assay that comprehensively probes the flux through de novo sphingolipid synthesis, post serine palmitoyltransferase, by monitoring the incorporation and metabolism of the 17 carbon dihydrosphingosine precursor with LC/MS. Pulse labeling and analysis of precursor metabolism identified sequential well-defined phases of sphingolipid synthesis, corresponding to the activity of different enzymes in the pathway, further confirmed by the use of specific inhibitors and modulators of sphingolipid metabolism. This work establishes precursor pulse labeling as a practical tool for comprehensively studying metabolic flux through de novo sphingolipid synthesis and complex sphingolipid generation.
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Affiliation(s)
- Justin M Snider
- Molecular and Cellular Biology and Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY; Departments of Medicine Stony Brook University, Stony Brook, NY; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY
| | - Ashley J Snider
- Departments of Medicine Stony Brook University, Stony Brook, NY; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY; Northport Veterans Affairs Medical Center, Northport, NY
| | - Lina M Obeid
- Departments of Medicine Stony Brook University, Stony Brook, NY; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY; Northport Veterans Affairs Medical Center, Northport, NY
| | - Chiara Luberto
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY; Physiology and Biophysics, Stony Brook University, Stony Brook, NY.
| | - Yusuf A Hannun
- Departments of Medicine Stony Brook University, Stony Brook, NY; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY.
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Schnute ME, McReynolds MD, Carroll J, Chrencik J, Highkin MK, Iyanar K, Jerome G, Rains JW, Saabye M, Scholten JA, Yates M, Nagiec MM. Discovery of a Potent and Selective Sphingosine Kinase 1 Inhibitor through the Molecular Combination of Chemotype-Distinct Screening Hits. J Med Chem 2017; 60:2562-2572. [DOI: 10.1021/acs.jmedchem.7b00070] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | | | | | - Jill Chrencik
- Medicine
Design, Pfizer, Groton, Connecticut 06340, United States
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12
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Kashem MA, Kennedy CA, Fogarty KE, Dimock JR, Zhang Y, Sanville-Ross ML, Skow DJ, Brunette SR, Swantek JL, Hummel HS, Swindle J, Nelson RM. A High-Throughput Genetic Complementation Assay in Yeast Cells Identified Selective Inhibitors of Sphingosine Kinase 1 Not Found Using a Cell-Free Enzyme Assay. Assay Drug Dev Technol 2016; 14:39-49. [DOI: 10.1089/adt.2015.671] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Mohammed A. Kashem
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Charles A. Kennedy
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Kylie E. Fogarty
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Janice R. Dimock
- Immunology and Respiratory Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Yunlong Zhang
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Mary L. Sanville-Ross
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Donna J. Skow
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Steven R. Brunette
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Jennifer L. Swantek
- Immunology and Respiratory Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | | | | | - Richard M. Nelson
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
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13
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Leveridge M, Collier L, Edge C, Hardwicke P, Leavens B, Ratcliffe S, Rees M, Stasi LP, Nadin A, Reith AD. A High-Throughput Screen to Identify LRRK2 Kinase Inhibitors for the Treatment of Parkinson’s Disease Using RapidFire Mass Spectrometry. ACTA ACUST UNITED AC 2015; 21:145-55. [DOI: 10.1177/1087057115606707] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/07/2015] [Indexed: 12/12/2022]
Abstract
LRRK2 is a large multidomain protein containing two functional enzymatic domains: a GTPase domain and a protein kinase domain. Dominant coding mutations in the LRRK2 protein are associated with Parkinson’s disease (PD). Among such pathogenic mutations, Gly2019Ser mutation in the LRRK2 kinase domain is the most frequent cause of familial PD in Caucasians and is also found in some apparently sporadic PD cases. This mutation results in 2- to 3-fold elevated LRRK2 kinase activity compared with wild type, providing a clear clinical hypothesis for the application of kinase inhibitors in the treatment of this disease. To date, reported screening assays for LRRK2 have been based on detection of labeled adenosine triphosphate and adenosine diphosphate or on antibody-based detection of phosphorylation events. While these assays do offer a high-throughput method of monitoring LRRK2 kinase activity, they are prone to interference from autofluorescent compounds and nonspecific events. Here we describe a label-free assay for LRRK2 kinase activity using the RapidFire mass spectrometry system. This assay format was found to be highly robust and enabled a screen of 100,000 lead-like small molecules. The assay successfully identified a number of known LRRK2 chemotypes that met stringent physicochemical criteria.
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Affiliation(s)
- Melanie Leveridge
- Department of Platform Technology and Science, GlaxoSmithKline Pharmaceuticals R&D, Hertfordshire, UK
| | - Lee Collier
- Department of Platform Technology and Science, GlaxoSmithKline Pharmaceuticals R&D, Hertfordshire, UK
- Cancer Research Technology, Babraham Research Campus, Cambridge, UK
| | - Colin Edge
- Department of Platform Technology and Science, GlaxoSmithKline Pharmaceuticals R&D, Hertfordshire, UK
| | - Phil Hardwicke
- Department of Platform Technology and Science, GlaxoSmithKline Pharmaceuticals R&D, Hertfordshire, UK
| | - Bill Leavens
- Department of Platform Technology and Science, GlaxoSmithKline Pharmaceuticals R&D, Hertfordshire, UK
| | - Steve Ratcliffe
- Department of Platform Technology and Science, GlaxoSmithKline Pharmaceuticals R&D, Hertfordshire, UK
| | - Mike Rees
- Department of Platform Technology and Science, GlaxoSmithKline Pharmaceuticals R&D, Hertfordshire, UK
| | - Luigi Piero Stasi
- Neurodegeneration DPU, Neurosciences Therapy Area Unit, GlaxoSmithKline, Pharmaceuticals R&D, Hertfordshire, UK, and Pudong, China
- Nuevolution A/S, Rønnegade 8, DK-2100 Copenhagen, Denmark
| | - Alan Nadin
- Department of Platform Technology and Science, GlaxoSmithKline Pharmaceuticals R&D, Hertfordshire, UK
| | - Alastair D. Reith
- Neurodegeneration DPU, Neurosciences Therapy Area Unit, GlaxoSmithKline, Pharmaceuticals R&D, Hertfordshire, UK, and Pudong, China
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14
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Gordon LJ, Allen M, Artursson P, Hann MM, Leavens BJ, Mateus A, Readshaw S, Valko K, Wayne GJ, West A. Direct Measurement of Intracellular Compound Concentration by RapidFire Mass Spectrometry Offers Insights into Cell Permeability. ACTA ACUST UNITED AC 2015; 21:156-64. [DOI: 10.1177/1087057115604141] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/06/2015] [Indexed: 11/16/2022]
Abstract
One of the key challenges facing early stage drug discovery is understanding the commonly observed difference between the activity of compounds in biochemical assays and cellular assays. Traditionally, indirect or estimated cell permeability measurements such as estimations from logP or artificial membrane permeability are used to explain the differences. The missing link is a direct measurement of intracellular compound concentration in whole cells. This can, in some circumstances, be estimated from the cellular activity, but this may also be problematic if cellular activity is weak or absent. Advances in sensitivity and throughput of analytical techniques have enabled us to develop a high-throughput assay for the measurement of intracellular compound concentration for routine use to support lead optimization. The assay uses a RapidFire-MS based readout of compound concentration in HeLa cells following incubation of cells with test compound. The initial assay validation was performed by ultra-high performance liquid chromatography tandem mass spectrometry, and the assay was subsequently transferred to RapidFire tandem mass spectrometry. Further miniaturization and optimization were performed to streamline the process, increase sample throughput, and reduce cycle time. This optimization has delivered a semi-automated platform with the potential of production scale compound profiling up to 100 compounds per day.
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Affiliation(s)
- Laurie J. Gordon
- Department of Biological Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Morven Allen
- Department of Biological Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP) at Chemical Biology Consortium, Uppsala, Sweden
| | - Michael M. Hann
- Department of Chemical Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Bill J. Leavens
- Department of Chemical Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - André Mateus
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Simon Readshaw
- Department of Chemical Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Klara Valko
- Department of Chemical Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Gareth J. Wayne
- Department of Target and Pathway Validation, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Andy West
- Department of Chemical Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
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15
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Rye PT, LaMarr WA. Measurement of glycolysis reactants by high-throughput solid phase extraction with tandem mass spectrometry: Characterization of pyrophosphate-dependent phosphofructokinase as a case study. Anal Biochem 2015; 482:40-7. [PMID: 25849585 DOI: 10.1016/j.ab.2015.03.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 02/26/2015] [Accepted: 03/28/2015] [Indexed: 01/28/2023]
Abstract
Glycolysis is a 10-step metabolic pathway involved in producing cellular energy. Many tumors exhibit accelerated glycolytic rates, and enzymes that participate in this pathway are focal points of cancer research. Here, a novel method for the measurement of glycolysis reactants from in vitro samples is presented. Fast and direct measurement is achieved by an automated system that couples on-line solid phase extraction (SPE) with tandem mass spectrometry (MS/MS). The single analytical method enables multiple reactants to be measured concurrently, sustains a cycle time of 8s, and permits the measurement of up to 10,000 samples per day. Concentration-response curves were conducted using standards for 10 metabolic intermediates, and the results demonstrate that the detection strategy has excellent sensitivity (average limit of detection = 5.4 nM), dynamic range (nanomolar to micromolar), and linear response (average R(2) = 0.998). To test the analysis method on reactions, pyrophosphate-dependent phosphofructokinase (PPi-PFK) was used as a model system. Data that corroborate the activation and inhibition of PPi-PFK are presented, and the ways in which SPE-MS/MS simplifies experimental design and interpretation are highlighted. In summary, the method for measuring metabolic intermediates described here demonstrates unprecedented speed, performance, and versatility.
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Affiliation(s)
- Peter T Rye
- Agilent Technologies, Wakefield, MA 01880, USA.
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16
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Xu YF, Lu W, Rabinowitz JD. Avoiding misannotation of in-source fragmentation products as cellular metabolites in liquid chromatography-mass spectrometry-based metabolomics. Anal Chem 2015; 87:2273-81. [PMID: 25591916 DOI: 10.1021/ac504118y] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) technology allows for rapid quantitation of cellular metabolites, with metabolites identified by mass spectrometry and chromatographic retention time. Recently, with the development of rapid scanning high-resolution high accuracy mass spectrometers and the desire for high throughput screening, minimal or no chromatographic separation has become increasingly popular. When analyzing complex cellular extracts, however, the lack of chromatographic separation could potentially result in misannotation of structurally related metabolites. Here, we show that, even using electrospray ionization, a soft ionization method, in-source fragmentation generates unwanted byproducts of identical mass to common metabolites. For example, nucleotide-triphosphates generate nucleotide-diphosphates, and hexose-phosphates generate triose-phosphates. We evaluated yeast intracellular metabolite extracts and found more than 20 cases of in-source fragments that mimic common metabolites. Accordingly, chromatographic separation is required for accurate quantitation of many common cellular metabolites.
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Affiliation(s)
- Yi-Fan Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University , Princeton, New Jersey 08544, United States
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17
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18
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Adam GC, Meng J, Rizzo JM, Amoss A, Lusen JW, Patel A, Riley D, Hunt R, Zuck P, Johnson EN, Uebele VN, Hermes JD. Use of high-throughput mass spectrometry to reduce false positives in protease uHTS screens. ACTA ACUST UNITED AC 2014; 20:212-22. [PMID: 25336354 DOI: 10.1177/1087057114555832] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As a label-free technology, mass spectrometry (MS) enables assays to be generated that monitor the conversion of substrates with native sequences to products without the requirement for substrate modifications or indirect detection methods. Although traditional liquid chromatography (LC)-MS methods are relatively slow for a high-throughput screening (HTS) paradigm, with cycle times typically ≥ 60 s per sample, the Agilent RapidFire High-Throughput Mass Spectrometry (HTMS) System, with a cycle time of 5-7 s per sample, enables rapid analysis of compound numbers compatible with HTS. By monitoring changes in mass directly, HTMS assays can be used as a triaging tool by eliminating large numbers of false positives resulting from fluorescent compound interference or from compounds interacting with hydrophobic fluorescent dyes appended to substrates. Herein, HTMS assays were developed for multiple protease programs, including cysteine, serine, and aspartyl proteases, and applied as a confirmatory assay. The confirmation rate for each protease assay averaged <30%, independent of the primary assay technology used (i.e., luminescent, fluorescent, and time-resolved fluorescent technologies). Importantly, >99% of compounds designed to inhibit the enzymes were confirmed by the corresponding HTMS assay. Hence, HTMS is an effective tool for removing detection-based false positives from ultrahigh-throughput screening, resulting in hit lists enriched in true actives for downstream dose response titrations and hit-to-lead efforts.
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Affiliation(s)
- Gregory C Adam
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Juncai Meng
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Joseph M Rizzo
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Adam Amoss
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Jeffrey W Lusen
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Amita Patel
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Daniel Riley
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Rachel Hunt
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Paul Zuck
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Eric N Johnson
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA Wuxi Apptech
| | - Victor N Uebele
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Jeffrey D Hermes
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
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19
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Zhang Y, Qiu L, Wang Y, Qin X, Li Z. High-throughput and high-sensitivity quantitative analysis of serum unsaturated fatty acids by chip-based nanoelectrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry: early stage diagnostic biomarkers of pancreatic cancer. Analyst 2014; 139:1697-706. [PMID: 24551873 DOI: 10.1039/c3an02130k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this study, Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) coupled with chip-based direct-infusion nanoelectrospray ionization source (CBDInanoESI) in a negative ion mode is first employed to evaluate the effect of serum and its corresponding supernatant matrixes on the recoveries of serum free fatty acids (FFAs) based on spike-and-recovery experimental strategy by adding analytes along with analog internal standard (IS). The recoveries between serum (69.8-115.6%) and the supernatant (73.6-99.0%) matrixes are almost identical. Multiple point internal standard calibration curves between the concentration ratios of individual fatty acids to ISs, (C(17:1) as IS of C(16:1), C(18:3), C(18:2), or C(18:1) or C(21:0) as IS of C(20:4) or C(22:6)) versus their corresponding intensity ratios were constructed for C(16:1), C(18:3), C(18:2), C(18:1), C(20:4) and C(22:6), respectively, with correlation coefficients of greater than 0.99, lower limits of detection between 0.3 and 1.8 nM, and intra- and inter-day precision (relative standard deviations <18%), along with the linear dynamic range of three orders of magnitude. Sequentially, this advanced analytical platform was applied to perform simultaneous quantitative and qualitative analysis of multiple targets, e.g., serum supernatant unsaturated FFAs from 361 participants including 95 patients with pancreatic cancer (PC), 61 patients with pancreatitis and 205 healthy controls. Experimental results indicate that the levels of C(18:1), C(18:2), C(18:3), C(20:4) and C(22:6), as well as the level ratios of C(18:2)/C(18:1) and C(18:3)/C(18:1) of the PC patients were significantly decreased compared with those of healthy controls and the patients with pancreatitis (p < 0.01). It is worth noting that the ratio of C(18:2)/C(18:1), polyunsaturated fatty acids (PUFAs) (C(18:2), C(18:3), C(20:4), and C(22:6)), panel a (C(16:1), C(18:3), C(18:2), C(20:4) and C(22:6)) and panel b (C(18:2)/C(18:1) and C(18:3)/C(18:1)) performed excellent diagnostic ability, with an area under the receiver operating characteristic curve of ≥0.869, sensitivity of ≥85.7%, and specificity of ≥86.7% for differentiating the early stage PC from non-cancer subjects, which are greatly higher than those of clinically used serum biomarker CA 19-9. More importantly, this platform can also provide a fast and easy way to quantify the levels of FFAs in less than 30 s per sample.
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Affiliation(s)
- Yaping Zhang
- Department of Biophysics and structural biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, PR China.
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20
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Sun S, Kennedy RT. Droplet electrospray ionization mass spectrometry for high throughput screening for enzyme inhibitors. Anal Chem 2014; 86:9309-14. [PMID: 25137241 PMCID: PMC4165461 DOI: 10.1021/ac502542z] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 08/19/2014] [Indexed: 12/20/2022]
Abstract
High throughput screening (HTS) is important for identifying molecules with desired properties. Mass spectrometry (MS) is potentially powerful for label-free HTS due to its high sensitivity, speed, and resolution. Segmented flow, where samples are manipulated as droplets separated by an immiscible fluid, is an intriguing format for high throughput MS because it can be used to reliably and precisely manipulate nanoliter volumes and can be directly coupled to electrospray ionization (ESI) MS for rapid analysis. In this study, we describe a "MS Plate Reader" that couples standard multiwell plate HTS workflow to droplet ESI-MS. The MS plate reader can reformat 3072 samples from eight 384-well plates into nanoliter droplets segmented by an immiscible oil at 4.5 samples/s and sequentially analyze them by MS at 2 samples/s. Using the system, a label-free screen for cathepsin B modulators against 1280 chemicals was completed in 45 min with a high Z-factor (>0.72) and no false positives (24 of 24 hits confirmed). The assay revealed 11 structures not previously linked to cathepsin inhibition. For even larger scale screening, reformatting and analysis could be conducted simultaneously, which would enable more than 145,000 samples to be analyzed in 1 day.
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Affiliation(s)
- Shuwen Sun
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Robert T. Kennedy
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
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21
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Shimada T, Kelly J, LaMarr WA, van Vlies N, Yasuda E, Mason RW, Mackenzie W, Kubaski F, Giugliani R, Chinen Y, Yamaguchi S, Suzuki Y, Orii KE, Fukao T, Orii T, Tomatsu S. Novel heparan sulfate assay by using automated high-throughput mass spectrometry: Application to monitoring and screening for mucopolysaccharidoses. Mol Genet Metab 2014; 113:92-9. [PMID: 25092413 PMCID: PMC4177953 DOI: 10.1016/j.ymgme.2014.07.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 07/09/2014] [Indexed: 01/02/2023]
Abstract
Mucopolysaccharidoses (MPS) are caused by deficiency of one of a group of specific lysosomal enzymes, resulting in excessive accumulation of glycosaminoglycans (GAGs). We previously developed GAG assay methods using liquid chromatography tandem mass spectrometry (LC-MS/MS); however, it takes 4-5 min per sample for analysis. For the large numbers of samples in a screening program, a more rapid process is desirable. The automated high-throughput mass spectrometry (HT-MS/MS) system (RapidFire) integrates a solid phase extraction robot to concentrate and desalt samples prior to direction into the MS/MS without chromatographic separation; thereby allowing each sample to be processed within 10s (enabling screening of more than one million samples per year). The aim of this study was to develop a higher throughput system to assay heparan sulfate (HS) using HT-MS/MS, and to compare its reproducibility, sensitivity and specificity with conventional LC-MS/MS. HS levels were measured in the blood (plasma and serum) from control subjects and patients with MPS II, III, or IV and in dried blood spots (DBS) from newborn controls and patients with MPS I, II, or III. Results obtained from HT-MS/MS showed 1) that there was a strong correlation of levels of disaccharides derived from HS in the blood, between those calculated using conventional LC-MS/MS and HT-MS/MS, 2) that levels of HS in the blood were significantly elevated in patients with MPS II and III, but not in MPS IVA, 3) that the level of HS in patients with a severe form of MPS II was higher than that in an attenuated form, 4) that reduction of blood HS level was observed in MPS II patients treated with enzyme replacement therapy or hematopoietic stem cell transplantation, and 5) that levels of HS in newborn DBS were elevated in patients with MPS I, II or III, compared to those of control newborns. In conclusion, HT-MS/MS provides much higher throughput than LC-MS/MS-based methods with similar sensitivity and specificity in an HS assay, indicating that HT-MS/MS may be feasible for diagnosis, monitoring, and newborn screening of MPS.
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Affiliation(s)
- Tsutomu Shimada
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE, USA
| | - Joan Kelly
- Agilent Technologies, Inc., Wakefield, MA, USA
| | | | - Naomi van Vlies
- Laboratory of Genetic Metabolic Disease, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Eriko Yasuda
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE, USA
| | - Robert W Mason
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE, USA
| | | | - Francyne Kubaski
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE, USA
| | - Roberto Giugliani
- Medical Genetics Service, HCPA and Department of Genetics, UFRGS, Porto Alegre, Brazil
| | - Yasutsugu Chinen
- Department of Pediatrics, Faculty of Medicine University of the Ryukyus, Okinawa, Japan
| | | | - Yasuyuki Suzuki
- Medical Education Development Center, Gifu University, Gifu, Japan
| | - Kenji E Orii
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Toshiyuki Fukao
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Tadao Orii
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Shunji Tomatsu
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE, USA; Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan.
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22
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Tomatsu S, Shimada T, Mason RW, Montaño AM, Kelly J, LaMarr WA, Kubaski F, Giugliani R, Guha A, Yasuda E, Mackenzie W, Yamaguchi S, Suzuki Y, Orii T. Establishment of glycosaminoglycan assays for mucopolysaccharidoses. Metabolites 2014; 4:655-79. [PMID: 25116756 PMCID: PMC4192686 DOI: 10.3390/metabo4030655] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/26/2014] [Accepted: 07/28/2014] [Indexed: 01/18/2023] Open
Abstract
Mucopolysaccharidoses (MPS) are a group of lysosomal storage disorders caused by deficiency of the lysosomal enzymes essential for catabolism of glycosaminoglycans (GAGs). Accumulation of undegraded GAGs results in dysfunction of multiple organs, resulting in distinct clinical manifestations. A range of methods have been developed to measure specific GAGs in various human samples to investigate diagnosis, prognosis, pathogenesis, GAG interaction with other molecules, and monitoring therapeutic efficacy. We established ELISA, liquid chromatography tandem mass spectrometry (LC-MS/MS), and an automated high-throughput mass spectrometry (HT-MS/MS) system (RapidFire) to identify epitopes (ELISA) or disaccharides (MS/MS) derived from different GAGs (dermatan sulfate, heparan sulfate, keratan sulfate, and/or chondroitin sulfate). These methods have a high sensitivity and specificity in GAG analysis, applicable to the analysis of blood, urine, tissues, and cells. ELISA is feasible, sensitive, and reproducible with the standard equipment. HT-MS/MS yields higher throughput than conventional LC-MS/MS-based methods while the HT-MS/MS system does not have a chromatographic step and cannot distinguish GAGs with identical molecular weights, leading to a limitation of measurements for some specific GAGs. Here we review the advantages and disadvantages of these methods for measuring GAG levels in biological specimens. We also describe an unexpected secondary elevation of keratan sulfate in patients with MPS that is an indirect consequence of disruption of catabolism of other GAGs.
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Affiliation(s)
- Shunji Tomatsu
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA.
| | - Tsutomu Shimada
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA.
| | - Robert W Mason
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA.
| | - Adriana M Montaño
- Department of Pediatrics, Saint Louis University, St. Louis, MO 63104, USA.
| | - Joan Kelly
- Agilent Technologies, Inc., Wakefield, MA 01880, USA.
| | | | - Francyne Kubaski
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA.
| | - Roberto Giugliani
- Department of Genetics/UFRGS, Medical Genetics Service/HCPA, Porto Alegre 90035-903, Brazil.
| | - Aratrik Guha
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA.
| | - Eriko Yasuda
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA.
| | - William Mackenzie
- Nemours/Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA.
| | - Seiji Yamaguchi
- Department of Pediatrics, Shimane University, Shimane 693-8501, Japan.
| | - Yasuyuki Suzuki
- Medical Education Development Center, Gifu University, Gifu 501-1194, Japan.
| | - Tadao Orii
- Department of Pediatrics, Gifu University, Gifu 501-1194, Japan.
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23
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Lima S, Milstien S, Spiegel S. A real-time high-throughput fluorescence assay for sphingosine kinases. J Lipid Res 2014; 55:1525-30. [PMID: 24792926 DOI: 10.1194/jlr.d048132] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Indexed: 11/20/2022] Open
Abstract
Sphingosine kinases (SphKs), of which there are two isoforms, SphK1 and SphK2, have been implicated in regulation of many important cellular processes. We have developed an assay for monitoring SphK1 and SphK2 activity in real time without the need for organic partitioning of products, radioactive materials, or specialized equipment. The assay conveniently follows SphK-dependent changes in 7-nitro-2-1,3-benzoxadiazol-4-yl (NBD)-labeled sphingosine (Sph) fluorescence and can be easily performed in 384-well plate format with small reaction volumes. We present data showing dose-proportional responses to enzyme, substrate, and inhibitor concentrations. The SphK1 and SphK2 binding affinities for NBD-Sph and the IC50 values of inhibitors determined were consistent with those reported with other methods. Because of the versatility and simplicity of the assay, it should facilitate the routine characterization of inhibitors and SphK mutants and can be readily used for compound library screening in high-throughput format.
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Affiliation(s)
- Santiago Lima
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Sheldon Milstien
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
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24
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Tomatsu S, Shimada T, Mason RW, Kelly J, LaMarr WA, Yasuda E, Shibata Y, Futatsumori H, Montaño AM, Yamaguchi S, Suzuki Y, Orii T. Assay for Glycosaminoglycans by Tandem Mass Spectrometry and its Applications. ACTA ACUST UNITED AC 2014; 2014:006. [PMID: 25068074 PMCID: PMC4109812 DOI: 10.4172/2155-9872.s2-006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Glycosaminoglycans (GAGs) are distributed in the whole body and play a variety of important physiological roles associated with inflammation, growth, coagulation, fibrinolysis, lipolysis, and cell-matrix biology. Accumulation of undegraded GAGs in lysosomes gives rise to a distinct clinical syndrome, mucopolysaccharidoses. Measurement of each specific GAG in a variety of specimens is urgently required to understand GAG interaction with other molecules, physiological status of patients, and prognosis and pathogenesis of the disease. We established a highly sensitive and accurate tandem mass spectrometry (LC-MS/MS) method for measurements of disaccharides derived from four specific GAGs [dermatan sulfate (DS), heparan sulfate (HS), keratan sulfate (KS), and chondroitin sulfate (CS)]. Disaccharides were produced by specific enzyme digestion of each GAG, and quantified by negative ion mode of multiple reaction monitoring. Subclasses of HS and GAGs with identical molecular weights can be separated using a Hypercarbcolumn (2.0 mm×50 mm, 5 μm) with an aectonitrile gradient in ammonium acetate (pH 11.0). We also developed a GAG assay by RapidFire with tandem mass spectrometry (RF-MS/MS). The RF system consists of an integrated solid phase extraction robot that binds and de-salts samples from assay plates and directly injects them into a MS/MS detector, reducing sample processing time to ten seconds. RF-MS/MS consequently yields much faster throughput than conventional LC-MS/MS-based methods. However, the RF system does not have a chromatographic step, and therefore, cannot distinguish GAGs that have identical molecular weights. Both methods can be applied to analysis of dried blood spots, blood, and urine specimens. In this article, we compare the assay methods for GAGs and describe their potential applications.
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Affiliation(s)
- Shunji Tomatsu
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Tsutomu Shimada
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Robert W Mason
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Joan Kelly
- Agilent Technologies, Inc., Wakefield, MA, USA
| | | | - Eriko Yasuda
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Yuniko Shibata
- Central Research Lab., R&D Div. Seikagaku Co. Tokyo, Japan
| | | | - Adriana M Montaño
- Department of Pediatrics, Saint Louis University, St. Louis, Missouri, USA
| | | | - Yasuyuki Suzuki
- Medical Education Development Center, Gifu University, Japan
| | - Tadao Orii
- Department of Pediatrics, Gifu University, Gifu, Japan
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25
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Lowe DM, Gee M, Haslam C, Leavens B, Christodoulou E, Hissey P, Hardwicke P, Argyrou A, Webster SP, Mole DJ, Wilson K, Binnie M, Yard BA, Dean T, Liddle J, Uings I, Hutchinson JP. Lead discovery for human kynurenine 3-monooxygenase by high-throughput RapidFire mass spectrometry. ACTA ACUST UNITED AC 2013; 19:508-15. [PMID: 24381207 DOI: 10.1177/1087057113518069] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Kynurenine 3-monooxygenase (KMO) is a therapeutically important target on the eukaryotic tryptophan catabolic pathway, where it converts L-kynurenine (Kyn) to 3-hydroxykynurenine (3-HK). We have cloned and expressed the human form of this membrane protein as a full-length GST-fusion in a recombinant baculovirus expression system. An enriched membrane preparation was used for a directed screen of approximately 78,000 compounds using a RapidFire mass spectrometry (RF-MS) assay. The RapidFire platform provides an automated solid-phase extraction system that gives a throughput of approximately 7 s per well to the mass spectrometer, where direct measurement of both the substrate and product allowed substrate conversion to be determined. The RF-MS methodology is insensitive to assay interference, other than where compounds have the same nominal mass as Kyn or 3-HK and produce the same mass transition on fragmentation. These instances could be identified by comparison with the product-only data. The screen ran with excellent performance (average Z' value 0.8) and provided several tractable hit series for further investigation.
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Affiliation(s)
- Denise M Lowe
- 1Department of Biological Sciences, GlaxoSmithKline, Stevenage, UK
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26
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Structure guided design of a series of sphingosine kinase (SphK) inhibitors. Bioorg Med Chem Lett 2013; 23:4608-16. [PMID: 23845219 DOI: 10.1016/j.bmcl.2013.06.030] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 06/04/2013] [Accepted: 06/11/2013] [Indexed: 11/21/2022]
Abstract
Sphingosine-1-phosphate (S1P) signaling plays a vital role in mitogenesis, cell migration and angiogenesis. Sphingosine kinases (SphKs) catalyze a key step in sphingomyelin metabolism that leads to the production of S1P. There are two isoforms of SphK and observations made with SphK deficient mice show the two isoforms can compensate for each other's loss. Thus, inhibition of both isoforms is likely required to block SphK dependent angiogenesis. A structure based approach was used to design and synthesize a series of SphK inhibitors resulting in the identification of the first potent inhibitors of both isoforms of human SphK. Additionally, to our knowledge, this series of inhibitors contains the only sufficiently potent inhibitors of murine SphK1 with suitable physico-chemical properties to pharmacologically interrogate the role of SphK1 in rodent models and to reproduce the phenotype of SphK1 (-/-) mice.
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27
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Razavi M, Frick LE, LaMarr WA, Pope ME, Miller CA, Anderson NL, Pearson TW. High-throughput SISCAPA quantitation of peptides from human plasma digests by ultrafast, liquid chromatography-free mass spectrometry. J Proteome Res 2012; 11:5642-9. [PMID: 23126378 DOI: 10.1021/pr300652v] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We investigated the utility of an SPE-MS/MS platform in combination with a modified SISCAPA workflow for chromatography-free MRM analysis of proteotypic peptides in digested human plasma. This combination of SISCAPA and SPE-MS/MS technology allows sensitive, MRM-based quantification of peptides from plasma digests with a sample cycle time of ∼7 s, a 300-fold improvement over typical MRM analyses with analysis times of 30-40 min that use liquid chromatography upstream of MS. The optimized system includes capture and enrichment to near purity of target proteotypic peptides using rigorously selected, high affinity, antipeptide monoclonal antibodies and reduction of background peptides using a novel treatment of magnetic bead immunoadsorbents. Using this method, we have successfully quantitated LPS-binding protein and mesothelin (concentrations of ∼5000 ng/mL and ∼10 ng/mL, respectively) in human plasma. The method eliminates the need for upstream liquid-chromatography and can be multiplexed, thus facilitating quantitative analysis of proteins, including biomarkers, in large sample sets. The method is ideal for high-throughput biomarker validation after affinity enrichment and has the potential for applications in clinical laboratories.
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Affiliation(s)
- Morteza Razavi
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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28
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Baker DL, Pham TCT, Sparks MA. Structure and catalytic function of sphingosine kinases: analysis by site-directed mutagenesis and enzyme kinetics. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1831:139-46. [PMID: 23000541 DOI: 10.1016/j.bbalip.2012.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 12/17/2022]
Abstract
Sphingosine kinases 1 and 2 (SK1 and SK2) generate the bioactive lipid mediator sphingosine 1-phosphate and as such play a significant role in cell fate and in human health and disease. Despite significant interest in and examination of the role played by SK enzymes in disease, comparatively little is currently known about the three-dimensional structure and catalytic mechanisms of these enzymes. To date, limited numbers of studies have used site directed mutagenesis and activity determinations to examine the roles of individual SK residues in substrate, calmodulin, and membrane binding, as well as activation via phosphorylation. Assays are currently available that allow for both single and bisubstrate kinetic analysis of mutant proteins that show normal, lowered and enhanced activity as compared to wild type controls. Additional studies will be required to build on this foundation to completely understand SK mediated substrate binding and phosphoryl group transfer. A deeper understanding of the SK catalytic mechanism, as well as SK interactions with potential small molecule inhibitors will be invaluable to the future design and identification of SK activity modulators as research tools and potential therapeutics. This article is part of a Special Issue entitled Advances in Lysophospholipid Research.
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Affiliation(s)
- Daniel L Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
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29
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Modulation of cellular S1P levels with a novel, potent and specific inhibitor of sphingosine kinase-1. Biochem J 2012; 444:79-88. [DOI: 10.1042/bj20111929] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
SphK (sphingosine kinase) is the major source of the bioactive lipid and GPCR (G-protein-coupled receptor) agonist S1P (sphingosine 1-phosphate). S1P promotes cell growth, survival and migration, and is a key regulator of lymphocyte trafficking. Inhibition of S1P signalling has been proposed as a strategy for treatment of inflammatory diseases and cancer. In the present paper we describe the discovery and characterization of PF-543, a novel cell-permeant inhibitor of SphK1. PF-543 inhibits SphK1 with a Ki of 3.6 nM, is sphingosine-competitive and is more than 100-fold selective for SphK1 over the SphK2 isoform. In 1483 head and neck carcinoma cells, which are characterized by high levels of SphK1 expression and an unusually high rate of S1P production, PF-543 decreased the level of endogenous S1P 10-fold with a proportional increase in the level of sphingosine. In contrast with past reports that show that the growth of many cancer cell lines is SphK1-dependent, specific inhibition of SphK1 had no effect on the proliferation and survival of 1483 cells, despite a dramatic change in the cellular S1P/sphingosine ratio. PF-543 was effective as a potent inhibitor of S1P formation in whole blood, indicating that the SphK1 isoform of sphingosine kinase is the major source of S1P in human blood. PF-543 is the most potent inhibitor of SphK1 described to date and it will be useful for dissecting specific roles of SphK1-driven S1P signalling.
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30
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Hutchinson SE, Leveridge MV, Heathcote ML, Francis P, Williams L, Gee M, Munoz-Muriedas J, Leavens B, Shillings A, Jones E, Homes P, Baddeley S, Chung CW, Bridges A, Argyrou A. Enabling Lead Discovery for Histone Lysine Demethylases by High-Throughput RapidFire Mass Spectrometry. ACTA ACUST UNITED AC 2011; 17:39-48. [DOI: 10.1177/1087057111416660] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A high-throughput RapidFire mass spectrometry assay is described for the JMJD2 family of Fe2+, O2, and α-ketoglutarate-dependent histone lysine demethylases. The assay employs a short amino acid peptide substrate, corresponding to the first 15 amino acid residues of histone H3, but mutated at two positions to increase assay sensitivity. The assay monitors the direct formation of the dimethylated-Lys9 product from the trimethylated-Lys9 peptide substrate. Monitoring the formation of the monomethylated and des-methylated peptide products is also possible. The assay was validated using known inhibitors of the histone lysine demethylases, including 2,4-pyridinedicarboxylic acid and an α-ketoglutarate analogue. With a sampling rate of 7 s per well, the RapidFire technology permitted the single-concentration screening of 101 226 compounds against JMJD2C in 10 days using two instruments, typically giving Z′ values of 0.75 to 0.85. Several compounds were identified of the 8-hydroxyquinoline chemotype, a known series of inhibitors of the Lys9-specific histone demethylases. The peptide also functions as a substrate for JMJD2A, JMJD2D, and JMJD2E, thus enabling the development of assays for all 3 enzymes to monitor progress in compound selectivity. The assay represents the first report of a RapidFire mass spectrometry assay for an epigenetics target.
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Affiliation(s)
| | | | | | | | - Laura Williams
- Departments of Biological Reagents and Assay Development
| | | | | | - Bill Leavens
- Analytical Chemistry, Platform Technology and Science, GlaxoSmithKline, Stevenage, UK
| | | | - Emma Jones
- Departments of Biological Reagents and Assay Development
| | - Paul Homes
- Departments of Biological Reagents and Assay Development
| | | | | | - Angela Bridges
- Departments of Biological Reagents and Assay Development
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