1
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Müller L, Burton AK, Tayler CL, Rowedder JE, Hutchinson JP, Peace S, Quayle JM, Leveridge MV, Annan RS, Trost M, Peltier-Heap RE, Dueñas ME. A high-throughput MALDI-TOF MS biochemical screen for small molecule inhibitors of the antigen aminopeptidase ERAP1. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:3-11. [PMID: 36414185 DOI: 10.1016/j.slasd.2022.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
MALDI-TOF MS is a powerful analytical technique that provides a fast and label-free readout for in vitro assays in the high-throughput screening (HTS) environment. Here, we describe the development of a novel, HTS compatible, MALDI-TOF MS-based drug discovery assay for the endoplasmic reticulum aminopeptidase 1 (ERAP1), an important target in immuno-oncology and auto-immune diseases. A MALDI-TOF MS assay was developed beginning with an already established ERAP1 RapidFire MS (RF MS) assay, where the peptide YTAFTIPSI is trimmed into the product TAFTIPSI. We noted low ionisation efficiency of these peptides in MALDI-TOF MS and hence incorporated arginine residues into the peptide sequences to improve ionisation. The optimal assay conditions were established with these new basic assay peptides on the MALDI-TOF MS platform and validated with known ERAP1 inhibitors. Assay stability, reproducibility and robustness was demonstrated on the MALDI-TOF MS platform. From a set of 699 confirmed ERAP1 binders, identified in a prior affinity selection mass spectrometry (ASMS) screen, active compounds were determined at single concentration and in a dose-response format with the new MALDI-TOF MS setup. Furthermore, to allow for platform performance comparison, the same compound set was tested on the established RF MS setup, as the new basic peptides showed fragmentation in ESI-MS. The two platforms showed a comparable performance, but the MALDI-TOF MS platform had several advantages, such as shorter sample cycle times, reduced reagent consumption, and a lower tight-binding limit.
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Affiliation(s)
- Leonie Müller
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom
| | - Amy K Burton
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Chloe L Tayler
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - James E Rowedder
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Jonathan P Hutchinson
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Simon Peace
- GSK, Medicinal Chemistry, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Julie M Quayle
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Melanie V Leveridge
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Roland S Annan
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Matthias Trost
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom.
| | | | - Maria Emilia Dueñas
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom.
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2
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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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3
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Naito Y. Quantitative analysis capability of DIUTHAME mass spectrometry verified by acetylcholinesterase enzyme-catalyzed reaction assays. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4895. [PMID: 36426802 DOI: 10.1002/jms.4895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) is advantageous for mass spectrometry applications where throughput is important. However, quantitative analysis is essentially problematic for MALDI-MS whose results depend on the intrinsically stochastic microcrystalline state of the matrix. High-throughput screening (HTS) of drug candidates is a typical example that requires high throughput. The application of MALDI-MS to HTS, which is quantitative analysis, imposes restrictions on designing an experimental system. Surface-assisted laser desorption/ionization (SALDI) methods, which do not depend on matrix crystal formation, are expected to be applied to quantitative analyses such as HTS. A recently developed one type of SALDI methods, desorption ionization using through hole alumina membrane (DIUTHAME), possesses a distinct feature that the surface microstructure effective for ionization is formed by through holes. In this study, the quantitative analysis capability of DIUTHAME was verified by applying DIUTHAME to enzyme-catalyzed reaction measurements, which are also used for HTS. Quantitative DIUTHAME-MS was conducted on various conditions of acetylcholinesterase-catalyzed reaction solutions containing cow milk as a substitute of biological media. Even for the enzyme-catalyzed reaction solutions containing complex additives that make the quantitative analysis extremely difficult, DIUTHAME based on the through hole structure enables quantitative measurements of the analytes by applying the reaction solutions to the back side of the laser exposed surface. In comparison with those obtained by MALDI-MS, the results obtained by DIUTHAME-MS showed less variability of data and delivered a better linearity of the Lineweaver-Burk plots and a more reasonable value of the Michaelis constant. Accordingly, it was demonstrated that DIUTHAME-MS possesses the quantitative analysis capability much better than that of MALDI-MS.
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Affiliation(s)
- Yasuhide Naito
- The Graduate School for the Creation of New Photonics Industries, Shizuoka, Japan
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4
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Nylon Membrane-Based Electromembrane Extraction Coupled with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for the Determination of Insulin. SEPARATIONS 2022. [DOI: 10.3390/separations9100286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A rapid and sensitive protein determination method that uses electromembrane extraction (EME) and is coupled with matrix-assisted laser desorption/ionization mass spectrometry (MALDI/MS) is developed. A flat nylon membrane is used to collect proteins from an aqueous solution and is directly analyzed by MALDI/MS after the addition of the MALDI matrix. Insulin is used as a model protein to investigate the optimum extraction of the parameters. The optimum EME conditions are obtained at 12 V of voltage, 10 min of extraction time, 12 mL sample volume, and 400 rpm agitation rate. The linear dynamic range (LDR) of insulin in an aqueous solution is in the range of 1.0–100.0 nM. The limit of detection (LOD) for insulin in an aqueous solution is 0.3 nM with 103-fold signal-to-noise (S/N) ratio enhancement. Furthermore, the applicability of this method to determine insulin in complicated sample matrices is also investigated. The LDR of insulin in human urine samples is in the range of 5.0–100.0 nM, and the LOD of insulin in urine samples is calculated to be 1.5 nM. The precision and accuracy of this method are evaluated at three different concentration levels, and the coefficient of variation (CV) and relative error are less than 6%. This approach is time-efficient and economical, as the flat membrane mode of EME coupled with MALDI/MS is suitable.
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5
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Marín-Rubio JL, Peltier-Heap RE, Dueñas ME, Heunis T, Dannoura A, Inns J, Scott J, Simpson AJ, Blair HJ, Heidenreich O, Allan JM, Watt JE, Martin MP, Saxty B, Trost M. A Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Assay Identifies Nilotinib as an Inhibitor of Inflammation in Acute Myeloid Leukemia. J Med Chem 2022; 65:12014-12030. [PMID: 36094045 PMCID: PMC9511480 DOI: 10.1021/acs.jmedchem.2c00671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Inflammatory responses are important in cancer, particularly
in the context of monocyte-rich aggressive myeloid neoplasm. We developed
a label-free cellular phenotypic drug discovery assay to identify
anti-inflammatory drugs in human monocytes derived from acute myeloid
leukemia (AML), by tracking several features ionizing from only 2500
cells using matrix-assisted laser desorption/ionization-time of flight
(MALDI-TOF) mass spectrometry. A proof-of-concept screen showed that
the BCR-ABL inhibitor nilotinib, but not the structurally similar
imatinib, blocks inflammatory responses. In order to identify the
cellular (off-)targets of nilotinib, we performed thermal proteome
profiling (TPP). Unlike imatinib, nilotinib and other later-generation
BCR-ABL inhibitors bind to p38α and inhibit the p38α-MK2/3
signaling axis, which suppressed pro-inflammatory cytokine expression,
cell adhesion, and innate immunity markers in activated monocytes
derived from AML. Thus, our study provides a tool for the discovery
of new anti-inflammatory drugs, which could contribute to the treatment
of inflammation in myeloid neoplasms and other diseases.
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Affiliation(s)
- José Luis Marín-Rubio
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Rachel E Peltier-Heap
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Maria Emilia Dueñas
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Tiaan Heunis
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Abeer Dannoura
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Joseph Inns
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Jonathan Scott
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - A John Simpson
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK.,Respiratory Medicine Unit, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Helen J Blair
- Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Olaf Heidenreich
- Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - James M Allan
- Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Jessica E Watt
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Mathew P Martin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Barbara Saxty
- LifeArc, SBC Open Innovation Campus, Stevenage SG1 2FX, UK
| | - Matthias Trost
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
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6
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Shou WZ. Acoustic ejection mass spectrometry: Development, applications, and future perspective. Biomed Chromatogr 2021; 36:e5278. [PMID: 34741338 DOI: 10.1002/bmc.5278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/22/2021] [Indexed: 12/27/2022]
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7
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Luu GT, Sanchez LM. Toward improvement of screening through mass spectrometry-based proteomics: ovarian cancer as a case study. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 469:116679. [PMID: 34744497 PMCID: PMC8570641 DOI: 10.1016/j.ijms.2021.116679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Ovarian cancer is one of the leading causes of cancer related deaths affecting United States women. Early-stage detection of ovarian cancer has been linked to increased survival, however, current screening methods, such as biomarker testing, have proven to be ineffective in doing so. Therefore, further developments are necessary to be able to achieve positive patient prognosis. Ongoing efforts are being made in biomarker discovery towards clinical applications in screening for early-stage ovarian cancer. In this perspective, we discuss and provide examples for several workflows employing mass spectrometry-based proteomics towards protein biomarker discovery and characterization in the context of ovarian cancer; workflows include protein identification and characterization as well as intact protein profiling. We also discuss the opportunities to merge these workflows for a multiplexed approach for biomarkers. Lastly, we provide our insight as to future developments that may serve to enhance biomarker discovery workflows while also considering translational potential.
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Affiliation(s)
- Gordon T Luu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High St. Santa Cruz, CA, 95064
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High St. Santa Cruz, CA, 95064
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8
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Morato NM, Le MT, Holden DT, Graham Cooks R. Automated High-Throughput System Combining Small-Scale Synthesis with Bioassays and Reaction Screening. SLAS Technol 2021; 26:555-571. [PMID: 34697962 DOI: 10.1177/24726303211047839] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Purdue Make It system is a unique automated platform capable of small-scale in situ synthesis, screening small-molecule reactions, and performing direct label-free bioassays. The platform is based on desorption electrospray ionization (DESI), an ambient ionization method that allows for minimal sample workup and is capable of accelerating reactions in secondary droplets, thus conferring unique advantages compared with other high-throughput screening technologies. By combining DESI with liquid handling robotics, the system achieves throughputs of more than 1 sample/s, handling up to 6144 samples in a single run. As little as 100 fmol/spot of analyte is required to perform both initial analysis by mass spectrometry (MS) and further MSn structural characterization. The data obtained are processed using custom software so that results are easily visualized as interactive heatmaps of reaction plates based on the peak intensities of m/z values of interest. In this paper, we review the system's capabilities as described in previous publications and demonstrate its utilization in two new high-throughput campaigns: (1) the screening of 188 unique combinatorial reactions (24 reaction types, 188 unique reaction mixtures) to determine reactivity trends and (2) label-free studies of the nicotinamide N-methyltransferase enzyme directly from the bioassay buffer. The system's versatility holds promise for several future directions, including the collection of secondary droplets containing the products from successful reaction screening measurements, the development of machine learning algorithms using data collected from compound library screening, and the adaption of a variety of relevant bioassays to high-throughput MS.
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Affiliation(s)
- Nicolás M Morato
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - MyPhuong T Le
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - Dylan T Holden
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - R Graham Cooks
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
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9
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Evaluating Different Storage Media for Identification of Taenia saginata Proglottids Using MALDI-TOF Mass Spectrometry. Microorganisms 2021; 9:microorganisms9102006. [PMID: 34683327 PMCID: PMC8539231 DOI: 10.3390/microorganisms9102006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 12/29/2022] Open
Abstract
Taenia saginata is a helminth that can cause taeniasis in humans and cysticercosis in cattle. A species-specific diagnosis and differentiation from related species (e.g., Taenia solium) is crucial for individual patient management and disease control programs. Diagnostic stool microscopy is limited by low sensitivity and does not allow discrimination between T. saginata and T. solium. Molecular diagnostic approaches are not routinely available outside research laboratories. Recently, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) was proposed as a potentially suitable technique for species-specific helminth diagnosis. However, standardized protocols and commercial databases for parasite identification are currently unavailable, and pre-analytical factors have not yet been assessed. The purpose of this study was to employ MALDI-TOF MS for the identification of T. saginata proglottids obtained from a human patient, and to assess the effects of different sample storage media on the technique’s diagnostic accuracy. We generated T. saginata-specific main spectral profiles and added them to an in-house database for MALDI-TOF MS-based diagnosis of different helminths. Based on protein spectra, T. saginata proglottids could be successfully differentiated from other helminths, as well as bacteria and fungi. Additionally, we analyzed T. saginata proglottids stored in (i) LC–MS grade water; (ii) 0.45% sodium chloride; (iii) 70% ethanol; and (iv) 37% formalin after 2, 4, 6, 8, 12, and 24 weeks of storage. MALDI-TOF MS correctly identified 97.2–99.7% of samples stored in water, sodium chloride, and ethanol, with log-score values ≥2.5, thus indicating reliable species identification. In contrast, no protein spectra were obtained for samples stored in formalin. We conclude that MALDI-TOF-MS can be successfully employed for the identification of T. saginata, and that water, sodium chloride, and ethanol are equally effective storage solutions for prolonged periods of at least 24 weeks.
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10
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De Cesare V, Moran J, Traynor R, Knebel A, Ritorto MS, Trost M, McLauchlan H, Hastie CJ, Davies P. High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry-based deubiquitylating enzyme assay for drug discovery. Nat Protoc 2020; 15:4034-4057. [PMID: 33139956 DOI: 10.1038/s41596-020-00405-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
Deubiquitylating enzymes (DUBs) play a vital role in the ubiquitin pathway by editing or removing ubiquitin from their substrate. As breakthroughs within the ubiquitin field continue to highlight the potential of deubiquitylating enzymes as drug targets, there is increasing demand for versatile high-throughput (HT) tools for the identification of potent and selective DUB modulators. Here we present the HT adaptation of the previously published MALDI-TOF-based DUB assay method. In a MALDI-TOF DUB assay, we quantitate the amount of mono-ubiquitin generated by the in vitro cleavage of ubiquitin chains by DUBs. The method has been specifically developed for use with nanoliter-dispensing robotics to meet drug discovery requirements for the screening of large and diverse compound libraries. Contrary to the most common DUB screening technologies currently available, the MALDI-TOF DUB assay combines the use of physiological substrates with the sensitivity and reliability of the mass spectrometry-based readout.
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Affiliation(s)
- Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.
| | - Jennifer Moran
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Ryan Traynor
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
| | - Maria Stella Ritorto
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.,Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, UK
| | - Hilary McLauchlan
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.
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11
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Liu C, Van Berkel GJ, Cox DM, Covey TR. Operational Modes and Speed Considerations of an Acoustic Droplet Dispenser for Mass Spectrometry. Anal Chem 2020; 92:15818-15826. [DOI: 10.1021/acs.analchem.0c02999] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Chang Liu
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | | | - David M. Cox
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Thomas R. Covey
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
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12
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Emanuelson C, Ankenbruck N, Deiters A, Yu MS. High-Throughput Amenable MALDI-MS Detection of RNA and DNA with On-Surface Analyte Enrichment Using Fluorous Partitioning. SLAS DISCOVERY 2020; 26:58-66. [PMID: 32988284 DOI: 10.1177/2472555220958391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
High-throughput matrix-assisted laser desorption/ionization mass spectrometry (HT-MALDI-MS) has garnered considerable attention within the drug discovery industry as an information-rich alternative to assays using light-based detection methods. To date, these efforts have been primarily focused on assays using protein or peptide substrates. Methods for RNA or DNA analysis by HT-MALDI-MS have not been extensively reported due to the challenges associated with MALDI-MS of oligonucleotides, including the propensity to form multiple salt adducts, low ionization potential, and ease of fragmentation. The objective of this work was to develop a platform suitable for HT-MS analysis of RNA and DNA substrates that overcomes these hurdles by combining on-surface sample preparation with soft ionization. This has been accomplished through the selective immobilization of fluorous-tagged oligonucleotides on a fluorous-modified MS target plate, followed by on-surface enrichment, matrix addition, and direct laser desorption/ionization, a process dubbed fluorous HT-MS (F-HT-MS). The work has resulted in methods by which RNA and DNA substrates can be detected at nanomolar concentrations from a typical assay buffer system using procedures that are amenable to full automation. The protocols were applied to an miRNA biogenesis assay, demonstrating its potential for RNA processes and thereby filling a prominent gap in RNA drug discovery: the paucity of in vitro functional assays.
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Affiliation(s)
- Cole Emanuelson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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13
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Belov AM, Kozole J, Bean MF, Machutta CA, Zhang G, Gao EN, Ghislain L, Datwani SS, Leveridge M, Annan RS. Acoustic Mist Ionization-Mass Spectrometry: A Comparison to Conventional High-Throughput Screening and Compound Profiling Platforms. Anal Chem 2020; 92:13847-13854. [DOI: 10.1021/acs.analchem.0c02508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Luke Ghislain
- Beckman Coulter Life Sciences, 170 Rose Orchard Way, San Jose, California 95134, United States
| | - Sammy S. Datwani
- Beckman Coulter Life Sciences, 170 Rose Orchard Way, San Jose, California 95134, United States
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14
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Wagner A, Zhang J, Liu C, Covey TR, Olah TV, Weller H(BN, Shou WZ. Ultrahigh-Throughput and Chromatography-Free Bioanalysis of Polar Analytes with Acoustic Ejection Mass Spectrometry. Anal Chem 2020; 92:13525-13531. [DOI: 10.1021/acs.analchem.0c03006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Andrew Wagner
- Bristol-Myers Squibb, 3551 Lawrenceville Princeton Road, Princeton, New Jersey 08648, United States
| | - Jun Zhang
- Bristol-Myers Squibb, 3551 Lawrenceville Princeton Road, Princeton, New Jersey 08648, United States
| | - Chang Liu
- Sciex, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Thomas R. Covey
- Sciex, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Timothy V. Olah
- Bristol-Myers Squibb, 3551 Lawrenceville Princeton Road, Princeton, New Jersey 08648, United States
| | - Harold (Bud) N. Weller
- Bristol-Myers Squibb, 3551 Lawrenceville Princeton Road, Princeton, New Jersey 08648, United States
| | - Wilson Z. Shou
- Bristol-Myers Squibb, 3551 Lawrenceville Princeton Road, Princeton, New Jersey 08648, United States
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15
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Gachumi G, Purves RW, Hopf C, El-Aneed A. Fast Quantification Without Conventional Chromatography, The Growing Power of Mass Spectrometry. Anal Chem 2020; 92:8628-8637. [PMID: 32510944 DOI: 10.1021/acs.analchem.0c00877] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry (MS) in hyphenated techniques is widely accepted as the gold standard quantitative tool in life sciences. However, MS possesses intrinsic analytical capabilities that allow it to be a stand-alone quantitative technique, particularly with current technological advancements. MS has a great potential for simplifying quantitative analysis without the need for tedious chromatographic separation. Its selectivity relies on multistage MS analysis (MSn), including tandem mass spectrometry (MS/MS), as well as the ever-growing advancements of high-resolution MS instruments. This perspective describes various analytical platforms that utilize MS as a stand-alone quantitative technique, namely, flow injection analysis (FIA), matrix assisted laser desorption ionization (MALDI), including MALDI-MS imaging and ion mobility, particularly high-field asymmetric waveform ion mobility spectrometry (FAIMS). When MS alone is not capable of providing reliable quantitative data, instead of conventional liquid chromatography (LC)-MS, the use of a guard column (i.e., fast chromatography) may be sufficient for quantification. Although the omission of chromatographic separation simplifies the analytical process, extra procedures may be needed during sample preparation and clean-up to address the issue of matrix effects. The discussion of this manuscript focuses on key parameters underlying the uniqueness of each technique for its application in quantitative analysis without the need for a chromatographic separation. In addition, the potential for each analytical strategy and its challenges are discussed as well as improvements needed to render them as mainstream quantitative analytical tools. Overcoming the hurdles for fully validating a quantitative method will allow MS alone to eventually become an indispensable quantitative tool for clinical and toxicological studies.
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Affiliation(s)
- George Gachumi
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan Canada, S7N 5E5
| | - Randy W Purves
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan Canada, S7N 5E5.,Centre for Veterinary Drug Residues, Canadian Food Inspection Agency, 116 Veterinary Rd, Saskatoon, Saskatchewan Canada, S7N 2R3
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Strasse 10, 68163 Mannheim, Germany
| | - Anas El-Aneed
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan Canada, S7N 5E5
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16
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Shou WZ. Current status and future directions of high-throughput ADME screening in drug discovery. J Pharm Anal 2020; 10:201-208. [PMID: 32612866 PMCID: PMC7322755 DOI: 10.1016/j.jpha.2020.05.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
During the last decade high-throughput in vitro absorption, distribution, metabolism and excretion (HT-ADME) screening has become an essential part of any drug discovery effort of synthetic molecules. The conduct of HT-ADME screening has been "industrialized" due to the extensive development of software and automation tools in cell culture, assay incubation, sample analysis and data analysis. The HT-ADME assay portfolio continues to expand in emerging areas such as drug-transporter interactions, early soft spot identification, and ADME screening of peptide drug candidates. Additionally, thanks to the very large and high-quality HT-ADME data sets available in many biopharma companies, in silico prediction of ADME properties using machine learning has also gained much momentum in recent years. In this review, we discuss the current state-of-the-art practices in HT-ADME screening including assay portfolio, assay automation, sample analysis, data processing, and prediction model building. In addition, we also offer perspectives in future development of this exciting field.
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Affiliation(s)
- Wilson Z. Shou
- Bristol-Myers Squibb, PO Box 4000, Princeton, NJ, 08540, USA
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17
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Heap RE, Segarra-Fas A, Blain AP, Findlay GM, Trost M. Profiling embryonic stem cell differentiation by MALDI TOF mass spectrometry: development of a reproducible and robust sample preparation workflow. Analyst 2020; 144:6371-6381. [PMID: 31566633 DOI: 10.1039/c9an00771g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
MALDI TOF mass spectrometry (MS) is widely used to characterise and biotype bacterial samples, but a complementary method for profiling of mammalian cells is still underdeveloped. Current approaches vary dramatically in their sample preparation methods and are not suitable for high-throughput studies. In this work, we present a universal workflow for mammalian cell MALDI TOF MS analysis and apply it to distinguish ground-state naïve and differentiating mouse embryonic stem cells (mESCs), which can be used as a model for drug discovery. We employed a systematic approach testing many parameters to evaluate how efficiently and reproducibly each method extracted unique mass features from four different human cell lines. These data enabled us to develop a unique mammalian cell MALDI TOF workflow involving a freeze-thaw cycle, methanol fixing and a CHCA matrix to generate spectra that robustly phenotype different cell lines and are highly reproducible in peak identification across replicate spectra. We applied our optimised workflow to distinguish naïve and differentiating populations using multivariate analysis and reproducibly identify unique features. We were also able to demonstrate the compatibility of our optimised method for current automated liquid handling technologies. Consequently, our MALDI TOF MS profiling method enables identification of unique features and robust phenotyping of mESC differentiation in under 1 hour from culture to analysis, which is significantly faster and cheaper when compared with conventional methods such as qPCR. This method has the potential to be automated and can in the future be applied to profile other cell types and expanded towards cellular MALDI TOF MS screening assays.
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Affiliation(s)
- Rachel E Heap
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK.
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18
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Krenkel H, Hartmane E, Piras C, Brown J, Morris M, Cramer R. Advancing Liquid Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Toward Ultrahigh-Throughput Analysis. Anal Chem 2020; 92:2931-2936. [PMID: 31967792 PMCID: PMC7145281 DOI: 10.1021/acs.analchem.9b05202] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Label-free high-throughput screening using mass spectrometry has the potential to provide rapid large-scale sample analysis at a speed of more than one sample per second. Such speed is important for compound library, assay and future clinical screening of millions of samples within a reasonable time frame. Herein, we present a liquid atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) setup for high-throughput large-scale sample analysis (>5 samples per second) for three substance classes (peptides, antibiotics, and lipids). Liquid support matrices (LSM) were used for the analysis of standard substances as well as complex biological fluids (milk). Throughput and analytical robustness were mainly dependent on the complexity of the sample composition and the current limitations of the commercial hardware. However, the ultimate limits of liquid AP-MALDI in sample throughput can be conservatively estimated to be beyond 10-20 samples per second. This level of analytical speed is highly competitive compared with other label-free MS methods, including electrospray ionization and solid state MALDI, as well as MS methods using multiplexing by labeling, which in principle can also be used in combination with liquid AP-MALDI MS.
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Affiliation(s)
- Henriette Krenkel
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Evita Hartmane
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Cristian Piras
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Jeffery Brown
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom.,Waters Corporation , Stamford Avenue , Wilmslow SK9 4AX , United Kingdom
| | - Michael Morris
- Waters Corporation , Stamford Avenue , Wilmslow SK9 4AX , United Kingdom
| | - Rainer Cramer
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
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19
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Weigt D, Parrish CA, Krueger JA, Oleykowski CA, Rendina AR, Hopf C. Mechanistic MALDI-TOF Cell-Based Assay for the Discovery of Potent and Specific Fatty Acid Synthase Inhibitors. Cell Chem Biol 2019; 26:1322-1331.e4. [PMID: 31279605 DOI: 10.1016/j.chembiol.2019.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 05/24/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022]
Abstract
Human cancers require fatty acid synthase (FASN)-dependent de novo long-chain fatty acid synthesis for proliferation. FASN is therefore an attractive drug target, but fast technologies for reliable label-free cellular compound profiling are lacking. Recently, MALDI-mass spectrometry (MALDI-MS) has emerged as an effective technology for discovery of recombinant protein target inhibitors. Here we present an automated, mechanistic MALDI-MS cell assay, which monitors accumulation of the FASN substrate, malonyl-coenzyme A (CoA), in whole cells with limited sample preparation. Profiling of inhibitors, including unpublished compounds, identified compound 1 as the most potent FASN inhibitor (1 nM in A549 cells) discovered to date. Moreover, cellular MALDI-MS assays enable parallel profiling of additional pathway metabolites. Surprisingly, several compounds triggered cytidine 5'-diphosphocholine (CDP-choline) but not malonyl-CoA accumulation indicating that they inhibit diacylglycerol generation but not FASN activity. Taken together, our study suggests that MALDI-MS cell assays may become important tools in drug profiling that provide additional mechanistic insights concerning compound action on metabolic pathways.
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Affiliation(s)
- David Weigt
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim Technical University, Paul-Wittsack-Strasse 10, 68163 Mannheim, Germany
| | - Cynthia A Parrish
- Medicinal Chemistry, GlaxoSmithKline, 1250 S Collegeville Road, Collegeville, PA 19426, USA
| | - Julie A Krueger
- Immuno-Oncology and Combinations Research Unit, GlaxoSmithKline, 1250 S Collegeville Road, Collegeville, PA 19426, USA
| | - Catherine A Oleykowski
- Immuno-Oncology and Combinations Research Unit, GlaxoSmithKline, 1250 S Collegeville Road, Collegeville, PA 19426, USA
| | - Alan R Rendina
- Screening, Profiling and Mechanistic Biology, GlaxoSmithKline, 1250 S Collegeville Road, Collegeville, PA 19426, USA
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim Technical University, Paul-Wittsack-Strasse 10, 68163 Mannheim, Germany.
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20
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Winter M, Bretschneider T, Thamm S, Kleiner C, Grabowski D, Chandler S, Ries R, Kley JT, Fowler D, Bartlett C, Binetti R, Broadwater J, Luippold AH, Bischoff D, Büttner FH. Chemical Derivatization Enables MALDI-TOF-Based High-Throughput Screening for Microbial Trimethylamine (TMA)-Lyase Inhibitors. SLAS DISCOVERY 2019; 24:766-777. [PMID: 31059309 DOI: 10.1177/2472555219838216] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microbial-dependent trimethylamine (TMA) generation from dietary precursors such as choline was recently linked to cardiovascular diseases (CVDs) as well as chronic kidney disease (CKD). Inhibition of TMA-generating enzymes in gut bacteria would be an innovative approach to treat these diseases. The potential to accurately quantify secreted TMA levels highlights the capacity of mass spectrometry (MS) for tracking microbial TMA-lyase activity. However, high-throughput screening (HTS) by conventional MS instrumentation is hampered by limited sample throughput. Recent advancement in liquid handling and instrumentation of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS provides an HTS-compatible MS technology. The deciphering of enzymatic reactions using this label-free readout has been successfully applied but has thus far been limited to peptide/protein-centric activity assays. Here, we demonstrate the versatile applicability of MALDI-TOF by tracking a small molecule within a highly complex sample background. The key to success for this concept was chemical derivatization of the target molecule enabling quantitative assessment of microbial TMA formation. Further, its potential was demonstrated in a side-by-side comparison to RapidFire-MS in a primary screen and subsequent dose-response experiments. Overall, the established assay enables the screening for microbial TMA-lyase inhibitors and serves as a proof of concept for the applicability of MALDI-TOF for demanding assay concepts per se.
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Affiliation(s)
- Martin Winter
- 1 Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Tom Bretschneider
- 1 Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Sven Thamm
- 1 Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Carola Kleiner
- 1 Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Daniel Grabowski
- 1 Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Sarah Chandler
- 1 Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Robert Ries
- 1 Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Jörg T Kley
- 2 Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Danielle Fowler
- 3 Cardiometabolic Diseases Research, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Christina Bartlett
- 3 Cardiometabolic Diseases Research, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Ralph Binetti
- 4 Cancer Immunology & Immune Modulation, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - John Broadwater
- 3 Cardiometabolic Diseases Research, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Andreas H Luippold
- 1 Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Daniel Bischoff
- 1 Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Frank H Büttner
- 1 Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
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21
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Winter M, Ries R, Kleiner C, Bischoff D, Luippold AH, Bretschneider T, Büttner FH. Automated MALDI Target Preparation Concept: Providing Ultra-High-Throughput Mass Spectrometry–Based Screening for Drug Discovery. SLAS Technol 2018; 24:209-221. [PMID: 30074850 DOI: 10.1177/2472630318791981] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Label-free, mass spectrometric (MS) deciphering of enzymatic reactions by direct analysis of substrate-to-product conversion provides the next step toward more physiological relevant assays within drug discovery campaigns. Reduced risk of suffering from compound interference combined with diminished necessity for tailored signal mediators emphasizes the valuable role of label-free readouts. However, MS-based detection has not hitherto met high-throughput screening (HTS) requirements because of the lack of HTS-compatible sample introduction. In the present study, we report on a fully automated liquid-handling concept built in-house to concatenate biochemical assays with matrix-assisted laser desorption/ionization time-of-flight closing this technological gap. The integrated reformatting from 384- to 1536-well format enables cycle times of 0.6 s/sample for automated spotting and 0.4 s/sample for MS analysis, matching the requirements of HTS compatibility. In-depth examination of spotting quality, quantification accuracy, and instrument robustness together with the implementation of a protein tyrosine phosphatase 1B (PTP1B) inhibitor screening (4896 compounds) demonstrate the potential of the heavily inquired HTS integration of the label-free MS readout. Overall, the presented data demonstrate that the introduced automation concept makes label-free MS-based readouts accessible for HTS within drug discovery campaigns but also in other research areas requiring ultrafast MS-based detection.
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Affiliation(s)
- Martin Winter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Robert Ries
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Carola Kleiner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Daniel Bischoff
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Andreas H. Luippold
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Tom Bretschneider
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Frank H. Büttner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
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22
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Weigt D, Sammour DA, Ulrich T, Munteanu B, Hopf C. Automated analysis of lipid drug-response markers by combined fast and high-resolution whole cell MALDI mass spectrometry biotyping. Sci Rep 2018; 8:11260. [PMID: 30050068 PMCID: PMC6062520 DOI: 10.1038/s41598-018-29677-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/13/2018] [Indexed: 12/20/2022] Open
Abstract
Recent advances in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry have enabled whole cell-MALDI mass spectrometry biotyping of drug-treated cultured cells for rapid monitoring of known abundant pharmacodynamic protein markers such as polyacetylated histones. In contrast, generic and automated analytical workflows for discovery of such pharmacodynamic markers, in particular lipid markers, and their use in cellular tests of drug-like compounds are still lacking. Here, we introduce such a workflow and demonstrate its utility for cellular drug-response monitoring of BCR-ABL tyrosine kinase inhibitors in K562 leukemia cells: First, low-molecular mass features indicating drug responses are computationally extracted from groups of MALDI-TOF mass spectra. Then, the lipids/metabolites corresponding to these features are identified by MALDI-Fourier transformation mass spectrometry. To demonstrate utility of the method, we identify the potassium adduct of phosphatidylcholine PC(36:1) as well as heme B, a marker for erythroid differentiation, as markers for a label-free MALDI MS-based test of cellular responses to BCR-ABL inhibitors. Taken together, these results suggest that MALDI-TOF mass spectrometry of lipids and other low molecular mass metabolites could support cell-based drug profiling.
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Affiliation(s)
- David Weigt
- Center for biomedical Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
- HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120, Heidelberg, Germany
| | - Denis A Sammour
- Center for biomedical Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
| | - Timon Ulrich
- Center for biomedical Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
| | - Bogdan Munteanu
- Center for biomedical Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
| | - Carsten Hopf
- Center for biomedical Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany.
- HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120, Heidelberg, Germany.
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23
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Winter M, Bretschneider T, Kleiner C, Ries R, Hehn JP, Redemann N, Luippold AH, Bischoff D, Büttner FH. Establishing MALDI-TOF as Versatile Drug Discovery Readout to Dissect the PTP1B Enzymatic Reaction. SLAS DISCOVERY 2018; 23:561-573. [DOI: 10.1177/2472555218759267] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Label-free, mass spectrometric (MS) detection is an emerging technology in the field of drug discovery. Unbiased deciphering of enzymatic reactions is a proficient advantage over conventional label-based readouts suffering from compound interference and intricate generation of tailored signal mediators. Significant evolvements of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, as well as associated liquid handling instrumentation, triggered extensive efforts in the drug discovery community to integrate the comprehensive MS readout into the high-throughput screening (HTS) portfolio. Providing speed, sensitivity, and accuracy comparable to those of conventional, label-based readouts, combined with merits of MS-based technologies, such as label-free parallelized measurement of multiple physiological components, emphasizes the advantages of MALDI-TOF for HTS approaches. Here we describe the assay development for the identification of protein tyrosine phosphatase 1B (PTP1B) inhibitors. In the context of this precious drug target, MALDI-TOF was integrated into the HTS environment and cross-compared with the well-established AlphaScreen technology. We demonstrate robust and accurate IC50 determination with high accordance to data generated by AlphaScreen. Additionally, a tailored MALDI-TOF assay was developed to monitor compound-dependent, irreversible modification of the active cysteine of PTP1B. Overall, the presented data proves the promising perspective for the integration of MALDI-TOF into drug discovery campaigns.
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Affiliation(s)
- Martin Winter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Tom Bretschneider
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Carola Kleiner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Robert Ries
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Jörg P. Hehn
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Norbert Redemann
- Cardio-Metabolic Diseases, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Andreas H. Luippold
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Daniel Bischoff
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Frank H. Büttner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
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24
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Cornett DS, Scholle MD. Advances in MALDI Mass Spectrometry within Drug Discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2017; 22:1179-1181. [PMID: 29153034 DOI: 10.1177/2472555217735067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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25
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Heap RE, Hope AG, Pearson LA, Reyskens KMSE, McElroy SP, Hastie CJ, Porter DW, Arthur JSC, Gray DW, Trost M. Identifying Inhibitors of Inflammation: A Novel High-Throughput MALDI-TOF Screening Assay for Salt-Inducible Kinases (SIKs). SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2017; 22:1193-1202. [PMID: 28692323 PMCID: PMC5700774 DOI: 10.1177/2472555217717473] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 03/30/2017] [Accepted: 06/06/2017] [Indexed: 12/12/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight (MALDI TOF) mass spectrometry has become a promising alternative for high-throughput drug discovery as new instruments offer high speed, flexibility and sensitivity, and the ability to measure physiological substrates label free. Here we developed and applied high-throughput MALDI TOF mass spectrometry to identify inhibitors of the salt-inducible kinase (SIK) family, which are interesting drug targets in the field of inflammatory disease as they control production of the anti-inflammatory cytokine interleukin-10 (IL-10) in macrophages. Using peptide substrates in in vitro kinase assays, we can show that hit identification of the MALDI TOF kinase assay correlates with indirect ADP-Hunter kinase assays. Moreover, we can show that both techniques generate comparable IC50 data for a number of hit compounds and known inhibitors of SIK kinases. We further take these inhibitors to a fluorescence-based cellular assay using the SIK activity-dependent translocation of CRTC3 into the nucleus, thereby providing a complete assay pipeline for the identification of SIK kinase inhibitors in vitro and in cells. Our data demonstrate that MALDI TOF mass spectrometry is fully applicable to high-throughput kinase screening, providing label-free data comparable to that of current high-throughput fluorescence assays.
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Affiliation(s)
- Rachel E. Heap
- MRC Protein Phosphorylation & Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Anthony G. Hope
- Drug Discovery Unit, University of Dundee, Dundee, Scotland, UK
| | | | | | | | - C. James Hastie
- MRC Protein Phosphorylation & Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
| | - David W. Porter
- Drug Discovery Unit, University of Dundee, Dundee, Scotland, UK
| | - J. Simon C. Arthur
- Division of Cell Signalling and Immunology, University of Dundee, Dundee, Scotland, UK
| | - David W. Gray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Matthias Trost
- MRC Protein Phosphorylation & Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
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26
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Beeman K, Baumgärtner J, Laubenheimer M, Hergesell K, Hoffmann M, Pehl U, Fischer F, Pieck JC. Integration of an In Situ MALDI-Based High-Throughput Screening Process: A Case Study with Receptor Tyrosine Kinase c-MET. SLAS DISCOVERY 2017; 22:1203-1210. [DOI: 10.1177/2472555217727701] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Mass spectrometry (MS) is known for its label-free detection of substrates and products from a variety of enzyme reactions. Recent hardware improvements have increased interest in the use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS for high-throughput drug discovery. Despite interest in this technology, several challenges remain and must be overcome before MALDI-MS can be integrated as an automated “in-line reader” for high-throughput drug discovery. Two such hurdles include in situ sample processing and deposition, as well as integration of MALDI-MS for enzymatic screening assays that usually contain high levels of MS-incompatible components. Here we adapt our c-MET kinase assay to optimize for MALDI-MS compatibility and test its feasibility for compound screening. The pros and cons of the Echo (Labcyte) as a transfer system for in situ MALDI-MS sample preparation are discussed. We demonstrate that this method generates robust data in a 1536-grid format. We use the MALDI-MS to directly measure the ratio of c-MET substrate and phosphorylated product to acquire IC50 curves and demonstrate that the pharmacology is unaffected. The resulting IC50 values correlate well between the common label-based capillary electrophoresis and the label-free MALDI-MS detection method. We predict that label-free MALDI-MS-based high-throughput screening will become increasingly important and more widely used for drug discovery.
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Affiliation(s)
- Katrin Beeman
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Jens Baumgärtner
- Analytics Healthcare, Biomolecule Analytics, Merck KGaA, Darmstadt, Germany
| | - Manuel Laubenheimer
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Karlheinz Hergesell
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Martin Hoffmann
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Ulrich Pehl
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Frank Fischer
- Analytics Healthcare, Biomolecule Analytics, Merck KGaA, Darmstadt, Germany
| | - Jan-Carsten Pieck
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
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