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Le SB, Nordborg A, Josefsen KD, Olsen SM, Sletta H. Cultivation of Mycolicibacterium spp. Mutants in Miniaturized and High-Throughput Format to Characterize Their Growth, Phytosterol Conversion Ability, and Resistance to the Steroid Products. Methods Mol Biol 2023; 2704:185-200. [PMID: 37642845 DOI: 10.1007/978-1-0716-3385-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
This chapter describes methods for cultivation and characterization of the growth of Mycolicibacterium spp. mutants in a microbioreactor system in the presence of steroids and/or phytosterols followed by high-throughput mass spectrometry analysis to describe their ability to convert phytosterols into the target steroid androstenedione (AD). We focus on Mycolicibacterium neoaurum NRRL B-3805 ΔkstD which can convert phytosterol into androstenedione (AD) as one of its major steroid products, and mutants thereof with increased tolerance towards this end-product. By using BioLector 48-well plates with optodes at the bottom of each well, bacterial growth can be monitored online despite the turbidity of the growth medium resulting from non-dissolved phytosterol and steroid particles. To cope with the large number of samples that accumulate during growth experiments in microbioreactors and similar formats (e.g., microtiter plates), protocols for extraction and subsequent RapidFire-MS analysis are presented. This reduces the analysis time per sample to 10 s from 10 min required for regular LC-MS analysis.
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Affiliation(s)
- Simone Balzer Le
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Anna Nordborg
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway.
| | | | - Silje Malene Olsen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Håvard Sletta
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Dittakavi S, Mahadevan L, Chandrashekar DV, Bhamidipati RK, Suresh J, Dhakshinamoorthy S, Li Z, Baerenz F, Tennagels N, Mullangi R. High-throughput screening assay for the quantification of Cer d18:1/16:0, d18:1/24:0, d18:1/24:1, d18:1/18:0, d18:1/14:0, d18:1/20:0, and d18:1/22:0 in HepG2 cells using RapidFire mass spectrometry. Biomed Chromatogr 2019; 34:e4790. [PMID: 31883352 DOI: 10.1002/bmc.4790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/26/2022]
Abstract
Ceramides are known to be involved in various biological processes with their physiological levels elevated in various disease conditions such as diabetes, Alzheimer's, atherosclerosis. To facilitate the rapid screening of Cer d18:1/16:0, d18:1/24:0, d18:1/24:1, d18:1/18:0, d18:1/14:0, d18:1/20:0, and d18:1/22:0 inhibition in HepG2 cells, a RapidFire coupled to tandem mass spectrometry (RF-MS/MS) method has been developed. The RF platform provides an automated solid-phase extraction system that gave a throughput of 12.6 s per sample to an MS/MS system using electrospray ionization under the positive ion mode. Chromatographic separation of Cer d18:1/16:0, d18:1/24:0, d18:1/24:1, d18:1/18:0, d18:1/14:0, d18:1/20:0, and d18:1/22:0 was achieved using a ternary gradient on C8 type E cartridge. The MS/MS ion transitions monitored were 538.2 → 264.2, 650.7 → 264.2, 648.6 → 264.2, 566.4 → 264.2, 510.4 → 264.2, 594.4 → 264.2, 622.5 → 264.2, and 552.3 → 250.2 for Cer d18:1/16:0, d18:1/24:0, d18:1/24:1, d18:1/18:0, d18:1/14:0, d18:1/20:0, d18:1/22:0, and the internal standard (Cer d17:1/18:0), respectively. The RF-MS/MS methodology showed an excellent performance with an average Z' value of 0.5-0.7. This is the first report of an RF-MS/MS assay for screening of ceramides which is amenable for high-throughput screening.
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Affiliation(s)
- Sreekanth Dittakavi
- Drug Metabolism and Pharmacokinetics, Jubilant Biosys, Industrial Suburb, Yeshwanthpur, Bengaluru, India
| | - Lavanya Mahadevan
- Department of Biology, Jubilant Biosys Ltd, Industrial Suburb, Yeshwanthpur, Bengaluru, India
| | - Devaraj V Chandrashekar
- Drug Metabolism and Pharmacokinetics, Jubilant Biosys, Industrial Suburb, Yeshwanthpur, Bengaluru, India
| | - Ravi Kanth Bhamidipati
- Drug Metabolism and Pharmacokinetics, Jubilant Biosys, Industrial Suburb, Yeshwanthpur, Bengaluru, India
| | - Juluri Suresh
- Department of Biology, Jubilant Biosys Ltd, Industrial Suburb, Yeshwanthpur, Bengaluru, India
| | | | - Ziyu Li
- Sanofi Research and Development, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Felix Baerenz
- Sanofi Research and Development, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Norbert Tennagels
- Sanofi Research and Development, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Ramesh Mullangi
- Drug Metabolism and Pharmacokinetics, Jubilant Biosys, Industrial Suburb, Yeshwanthpur, Bengaluru, India
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Bretschneider T, Ozbal C, Holstein M, Winter M, Buettner FH, Thamm S, Bischoff D, Luippold AH. RapidFire BLAZE-Mode Is Boosting ESI-MS Toward High-Throughput-Screening. SLAS Technol 2019; 24:386-393. [PMID: 30698995 DOI: 10.1177/2472630318822449] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Label-free in vitro potency assays are an emerging field in drug discovery to enable more physiological conditions, to improve the readout quality, and to save time. For this approach mass spectrometry (MS) is a powerful technology to directly follow physiological processes. The speed of this methodology, however, was for a long time not compatible with chemiluminescence- or fluorescence-based assays. Recent advances in matrix-assisted laser desorption/ionization (MALDI) instrumentation paved the way for high-throughput MS analysis of label-free assays for large compound libraries, whereas electrospray ionization (ESI)-based mass spectrometers equipped with RapidFire autosamplers were limited to medium throughput. Here we present a technological advancement of the RapidFire device to enable cycle times of 2.5 s per sample. This newly developed BLAZE-mode substantially boosted the ESI-MS analysis speed, providing an alternative technology for label-free high-throughput screening.
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Affiliation(s)
- Tom Bretschneider
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Can Ozbal
- 2 PureHoney Technologies, Billerica, MA, USA
| | - Markus Holstein
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Martin Winter
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Frank H Buettner
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Sven Thamm
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Daniel Bischoff
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Andreas H Luippold
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
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6
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Bretschneider T, Luippold AH, Romig H, Bischoff D, Klinder K, Nicklin P, Rist W. Ultrafast and Predictive Mass Spectrometry-Based Autotaxin Assays for Label-Free Potency Screening. SLAS Discov 2017; 22:425-432. [PMID: 28328321 DOI: 10.1177/2472555217690484] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Autotaxin (ATX) is a promising drug target for the treatment of several diseases, such as cancer and fibrosis. ATX hydrolyzes lysophosphatidyl choline (LPC) into bioactive lysophosphatidic acid (LPA). The potency of ATX inhibitors can be readily determined by using fluorescence-based LPC derivatives. While such assays are ultra-high throughput, they are prone to false positives compared to assays based on natural LPC. Here we report the development of ultrafast mass spectrometry-based ATX assays enabling the measurement of data points within 13 s, which is 10 times faster than classic liquid chromatography-mass spectrometry. To this end, we set up a novel in vitro and whole-blood assay. We demonstrate that the potencies determined with these assays are in good agreement with the in vivo efficacy and that the whole-blood assay has the best predictive power. This high-throughput label-free approach paired with the translatable data quality is highly attractive for appropriate guidance of medicinal chemists for constructing strong structure-activity relationships.
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Affiliation(s)
- Tom Bretschneider
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | | | - Helmut Romig
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Daniel Bischoff
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Klaus Klinder
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Paul Nicklin
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Wolfgang Rist
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
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7
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Lu H, Kopcho L, Ghosh K, Witmer M, Parker M, Gupta S, Paul M, Krishnamurthy P, Laksmaiah B, Xie D, Tredup J, Zhang L, Abell LM. Development of a RapidFire mass spectrometry assay and a fluorescence assay for the discovery of kynurenine aminotransferase II inhibitors to treat central nervous system disorders. Anal Biochem 2016; 501:56-65. [PMID: 26874021 DOI: 10.1016/j.ab.2016.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/15/2016] [Accepted: 02/02/2016] [Indexed: 12/16/2022]
Abstract
Kynurenine aminotransferases convert kynurenine to kynurenic acid and play an important role in the tryptophan degradation pathway. Kynurenic acid levels in brain have been hypothesized to be linked to a number of central nervous system (CNS) disorders. Kynurenine aminotransferase II (KATII) has proven to be a key modulator of kynurenic acid levels in brain and, thus, is an attractive target to treat CNS diseases. A sensitive, high-throughput, label-free RapidFire mass spectrometry assay has been developed for human KATII. Unlike other assays, this method is directly applicable to KATII enzymes from different animal species, which allows us to select proper animal model(s) to evaluate human KATII inhibitors. We also established a coupled fluorescence assay for human KATII. The short assay time and kinetic capability of the fluorescence assay provide a useful tool for orthogonal inhibitor validation and mechanistic studies.
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Affiliation(s)
- Hao Lu
- Lead Discovery and Optimization, Bristol-Myers Squibb R&D, Pennington, NJ 08534, USA.
| | - Lisa Kopcho
- Lead Discovery and Optimization, Bristol-Myers Squibb R&D, Pennington, NJ 08534, USA
| | - Kaushik Ghosh
- Disease Sciences and Technology, Biocon Bristol-Myers Squibb R&D Centre, Bangalore, 560099, India
| | - Mark Witmer
- Protein Science, Bristol-Myers Squibb R&D, Princeton, NJ 08648, USA
| | - Michael Parker
- Discovery Chemistry, Bristol-Myers Squibb R&D, Wallingford, CT 06492, USA
| | - Sumit Gupta
- Disease Sciences and Technology, Biocon Bristol-Myers Squibb R&D Centre, Bangalore, 560099, India
| | - Marilyn Paul
- Disease Sciences and Technology, Biocon Bristol-Myers Squibb R&D Centre, Bangalore, 560099, India
| | - Prasad Krishnamurthy
- Disease Sciences and Technology, Biocon Bristol-Myers Squibb R&D Centre, Bangalore, 560099, India
| | - Basanth Laksmaiah
- Disease Sciences and Technology, Biocon Bristol-Myers Squibb R&D Centre, Bangalore, 560099, India
| | - Dianlin Xie
- Protein Science, Bristol-Myers Squibb R&D, Princeton, NJ 08648, USA
| | - Jeffrey Tredup
- Protein Science, Bristol-Myers Squibb R&D, Princeton, NJ 08648, USA
| | - Litao Zhang
- Lead Discovery and Optimization, Bristol-Myers Squibb R&D, Pennington, NJ 08534, USA
| | - Lynn M Abell
- Lead Discovery and Optimization, Bristol-Myers Squibb R&D, Pennington, NJ 08534, USA.
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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