1
|
Williams JD, Pu F, Sawicki JW, Elsen NL. Ultra-high-throughput mass spectrometry in drug discovery: fundamentals and recent advances. Expert Opin Drug Discov 2024; 19:291-301. [PMID: 38111363 DOI: 10.1080/17460441.2023.2293153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
INTRODUCTION Ultra-high-throughput mass spectrometry, uHT-MS, is a technology that utilizes ionization and sample delivery technologies optimized to enable sampling from well plates at > 1 sample per second. These technologies do not need a chromatographic separation step and can be utilized in a wide variety of assays to detect a broad range of analytes including small molecules, lipids, and proteins. AREAS COVERED This manuscript provides a brief historical review of high-throughput mass spectrometry and the recently developed technologies that have enabled uHT-MS. The report also provides examples and references on how uHT-MS has been used in biochemical and chemical assays, nuisance compound profiling, protein analysis and high throughput experimentation for chemical synthesis. EXPERT OPINION The fast analysis time provided by uHT-MS is transforming how biochemical and chemical assays are performed in drug discovery. The potential to associate phenotypic responses produced by 1000's of compound treatments with changes in endogenous metabolite and lipid signals is becoming feasible. With the augmentation of simple, fast, high-throughput sample preparation, the scope of uHT-MS usage will increase. However, it likely will not supplant LC-MS for analyses that require low detection limits from complex matrices or characterization of complex biotherapeutics such as antibody-drug conjugates.
Collapse
Affiliation(s)
| | - Fan Pu
- Abbvie Discovery Research, North Chicago, IL, USA
| | | | | |
Collapse
|
2
|
Šebela M. The use of matrix-assisted laser desorption/ionization mass spectrometry in enzyme activity assays and its position in the context of other available methods. MASS SPECTROMETRY REVIEWS 2023; 42:1008-1031. [PMID: 34549449 DOI: 10.1002/mas.21733] [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: 04/08/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Activity assays are indispensable for studying biochemical properties of enzymes. The purposes of measuring activity are wide ranging from a simple detection of the presence of an enzyme to kinetic experiments evaluating the substrate specificity, reaction mechanisms, and susceptibility to inhibitors. Common activity assay methods include spectroscopy, electrochemical sensors, or liquid chromatography coupled with various detection techniques. This review focuses on the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a growing and modern alternative, which offers high speed of analysis, sensitivity, versatility, possibility of automation, and cost-effectiveness. It may reveal reaction intermediates, side products or measure more enzymes at once. The addition of an internal standard or calculating the ratios of the substrate and product peak intensities and areas overcome the inherent inhomogeneous distribution of analyte and matrix in the sample spot, which otherwise results in a poor reproducibility. Examples of the application of MALDI-TOF MS for assaying hydrolases (including peptidases and β-lactamases for antibiotic resistance tests) and other enzymes are provided. Concluding remarks summarize advantages and challenges coming from the present experience, and draw future perspectives such as a screening of large libraries of chemical compounds for their substrate or inhibitory properties towards enzymes.
Collapse
Affiliation(s)
- Marek Šebela
- Department of Biochemistry, Faculty of Science, and CATRIN, Palacký University, Olomouc, Czech Republic
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Screening assays for tyrosine kinase inhibitors:A review. J Pharm Biomed Anal 2022; 223:115166. [DOI: 10.1016/j.jpba.2022.115166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022]
|
5
|
Repurposing of pharmaceutical drugs by high-throughput approach for antihypertensive activity as inhibitors of angiotensin-converting enzyme (ACE) using HPLC-ESI-MS/MS method. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
6
|
McLaren DG, Shah V, Wisniewski T, Ghislain L, Liu C, Zhang H, Saldanha SA. High-Throughput Mass Spectrometry for Hit Identification: Current Landscape and Future Perspectives. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:168-191. [PMID: 33482074 DOI: 10.1177/2472555220980696] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
For nearly two decades mass spectrometry has been used as a label-free, direct-detection method for both functional and affinity-based screening of a wide range of therapeutically relevant target classes. Here, we present an overview of several established and emerging mass spectrometry platforms and summarize the unique strengths and performance characteristics of each as they apply to high-throughput screening. Multiple examples from the recent literature are highlighted in order to illustrate the power of each individual technique, with special emphasis given to cases where the use of mass spectrometry was found to be differentiating when compared with other detection formats. Indeed, as many of these examples will demonstrate, the inherent strengths of mass spectrometry-sensitivity, specificity, wide dynamic range, and amenability to complex matrices-can be leveraged to enhance the discriminating power and physiological relevance of assays included in screening cascades. It is our hope that this review will serve as a useful guide to readers of all backgrounds and experience levels on the applicability and benefits of mass spectrometry in the search for hits, leads, and, ultimately, drugs.
Collapse
|
7
|
p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Nat Chem Biol 2020; 16:1078-1086. [DOI: 10.1038/s41589-020-0600-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/25/2020] [Indexed: 12/19/2022]
|
8
|
Ling L, Xiao C, Wang S, Guo L, Guo X. A pyrene linked peptide probe for quantitative analysis of protease activity via MALDI-TOF-MS. Talanta 2019; 200:236-241. [DOI: 10.1016/j.talanta.2019.03.055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/27/2019] [Accepted: 03/14/2019] [Indexed: 12/12/2022]
|
9
|
Abu-Dieyeh MH, Alduroobi HM, Al-Ghouti MA. Potential of mercury-tolerant bacteria for bio-uptake of mercury leached from discarded fluorescent lamps. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 237:217-227. [PMID: 30798040 DOI: 10.1016/j.jenvman.2019.02.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/23/2019] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
In this study, ten bacterial strains were found to be mercury resistant after their isolation from Qatari coastal sediments. Tolerance was found to be up to 100-150 ppm for five strains. Those strains had optimum growth conditions at salinity level of 10 ppm NaCl and pH 7-8. Starting from a concentration 7.9 ppm of mercury extracted from fluorescent lamps and after 6 days of incubation at 37 °C, two isolated strains HA6 (Bacillus spp.) and HA9 (Acinetobacter sp.) showed 96.7% and 98.9% of mercury bio-uptake efficiency, respectively. Other strains were capable of removing more than 60% of extracted mercury.
Collapse
Affiliation(s)
- Mohammed H Abu-Dieyeh
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar
| | - Haya M Alduroobi
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar
| | - Mohammad A Al-Ghouti
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar.
| |
Collapse
|
10
|
Tao M, Zhang L, Guo Y. Dual-Channel Enzymatic Inhibition Measurement (DEIM) Coupling Isotope Substrate via Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2427-2435. [PMID: 30159674 DOI: 10.1007/s13361-018-2054-3] [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: 04/21/2018] [Revised: 07/20/2018] [Accepted: 08/04/2018] [Indexed: 06/08/2023]
Abstract
A novel dual-channel enzymatic inhibition measurement (DEIM) method was developed to improve the repeatability with light/heavy isotope substrates, producing reliable relative standard deviations (< 3%) by employing acetylcholinesterase (AChE) as the model enzyme. The matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) was adapted for enzyme-inhibited method due to its good salt-tolerance and high throughput; meanwhile, dual-channel enzymatic reactions were performed to improve the repeatability of each well. The acetylcholinesterase inhibition measurement was conducted by mixing the quenched enzyme reaction solution of blank group (with heavy isotope as substrate) and experimental group (with light isotope as substrate), of which the inhibition rate might be affected by isotope effects. Hence, inverse study and Km measurement were implemented to validate the method. The inverse study shows similar inhibition rate (68.9 and 70.3%) and the Km of isotope substrates are analogous (0.139 and 0.135 mM), which demonstrated that the novel method is feasible to AChE inhibition measurement. Finally, the method was applied to herb extracts, half of which exhibit inhibition to AChE. The precise dual-channel enzymatic inhibition measurement (DEIM) method could be regarded as a promising approach to potential enzyme inhibitor screening. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Min Tao
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, Center for Excellence in Molecular Synthesis, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, People's Republic of China
- Postdoctoral Programme, Mayinglong Pharmaceutical Group Co. Ltd., Wuhan, People's Republic of China
| | - Li Zhang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, Center for Excellence in Molecular Synthesis, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, People's Republic of China.
| | - Yinlong Guo
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, Center for Excellence in Molecular Synthesis, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, People's Republic of China.
| |
Collapse
|
11
|
Jerome Jeyakumar JM, Zhang M, Thiruvengadam M. Determination of mycotoxins by HPLC, LC-ESI-MS/MS, and MALDI-TOF MS in Fusarium species-infected sugarcane. Microb Pathog 2018; 123:98-110. [DOI: 10.1016/j.micpath.2018.06.045] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/16/2018] [Accepted: 06/28/2018] [Indexed: 01/12/2023]
|
12
|
Machálková M, Schejbal J, Glatz Z, Preisler J. A label-free MALDI TOF MS-based method for studying the kinetics and inhibitor screening of the Alzheimer’s disease drug target β-secretase. Anal Bioanal Chem 2018; 410:7441-7448. [DOI: 10.1007/s00216-018-1354-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/21/2018] [Accepted: 08/30/2018] [Indexed: 01/19/2023]
|
13
|
Rapid LC-MS Based High-Throughput Screening Method, Affording No False Positives or False Negatives, Identifies a New Inhibitor for Carbonic Anhydrase. Sci Rep 2017; 7:10324. [PMID: 28871149 PMCID: PMC5583356 DOI: 10.1038/s41598-017-08602-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/12/2017] [Indexed: 12/03/2022] Open
Abstract
Developing effective high-throughput screening (HTS) methods is of paramount importance in the early stage of drug discovery. While rugged and robust assays may be easily developed for certain enzymes, HTS assays designed to identify ligands that block protein binding are much more challenging to develop; attenuating the number of false positives and false negatives under high-throughput screening conditions is particularly difficult. We describe an MS-based HTS workflow that addresses these challenges. The assay mitigates false positives by selectively identifying positive hits exclusively when a ligand at the binding site of interest is displaced; it mitigates false negatives by detecting a reporter compound that ionizes well, not by detecting the ligand binder, which may not ionize. The method was validated by detecting known binders of three proteins, pepsin, maltose binding protein (MBP), and carbonic anhydrase (CA) in the presence of hundreds of non-binders. We also identified a novel CA binder, pifithrin-µ, which could not have been identified by any other MS-based assay because of its poor ionization efficiency. This new method addresses many of the challenges that are currently encountered during high-throughput screening.
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Musharraf SG, Bhatti MS, Choudhary MI, Rahman AU. Screening of inhibitors of angiotensin-converting enzyme (ACE) employing high performance liquid chromatography-electrospray ionization triple quadrupole mass spectrometry (HPLC-ESI-QqQ-MS). Eur J Pharm Sci 2017; 101:182-188. [DOI: 10.1016/j.ejps.2017.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 11/15/2022]
|
16
|
Forbes CD, Toth JG, Ozbal CC, Lamarr WA, Pendleton JA, Rocks S, Gedrich RW, Osterman DG, Landro JA, Lumb KJ. High-Throughput Mass Spectrometry Screening for Inhibitors of Phosphatidylserine Decarboxylase. ACTA ACUST UNITED AC 2016; 12:628-34. [PMID: 17478478 DOI: 10.1177/1087057107301320] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A high-throughput mass spectrometry assay to measure the catalytic activity of phosphatidylserine decarboxylase (PISD) is described. PISD converts phosphatidylserine to phosphatidylethanolamine during lipid synthesis. Traditional methods of measuring PISD activity are low throughput and unsuitable for the high-throughput screening of large compound libraries. The high-throughput mass spectrometry assay directly measures phosphatidylserine and phosphatidylethanolamine using the RapidFire™ platform at a rate of 1 sample every 7.5 s. The assay is robust, with an average Z′ value of 0.79 from a screen of 9920 compounds. Of 60 compounds selected for confirmation, 54 are active in dose-response studies. The application of high-throughput mass spectrometry permitted a high-quality screen to be performed for an otherwise intractable target. ( Journal of Biomolecular Screening 2007:628-634)
Collapse
Affiliation(s)
- Chris D Forbes
- Department of Research Technologies, Bayer Pharmaceuticals Corporation, West Haven, CT 06516, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Lee J, Park IS, Park G, Cho K, Park HS, Min DH. A robust and quantitative assay platform for multiplexed, high throughput screening of protein kinase inhibitors. Chem Commun (Camb) 2016; 52:12112-12115. [DOI: 10.1039/c6cc05834e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a new platform for multiplexed protein kinase activity assay using TiO2decorated graphene oxide (GO), which is applicable to high throughput inhibitor screening.
Collapse
Affiliation(s)
- Jieon Lee
- Center for RNA Research
- Institute for Basic Science
- Department of Chemistry
- Seoul National University
- Seoul
| | - Il-Soo Park
- Center for RNA Research
- Institute for Basic Science
- Department of Chemistry
- Seoul National University
- Seoul
| | - Ginam Park
- Center for RNA Research
- Institute for Basic Science
- Department of Chemistry
- Seoul National University
- Seoul
| | - Kyukwang Cho
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon
- Korea
| | - Hee-Sung Park
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon
- Korea
| | - Dal-Hee Min
- Center for RNA Research
- Institute for Basic Science
- Department of Chemistry
- Seoul National University
- Seoul
| |
Collapse
|
18
|
Haslam C, Hellicar J, Dunn A, Fuetterer A, Hardy N, Marshall P, Paape R, Pemberton M, Resemannand A, Leveridge M. The Evolution of MALDI-TOF Mass Spectrometry toward Ultra-High-Throughput Screening: 1536-Well Format and Beyond. ACTA ACUST UNITED AC 2015; 21:176-86. [DOI: 10.1177/1087057115608605] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/30/2015] [Indexed: 12/11/2022]
Abstract
Mass spectrometry (MS) offers a label-free, direct-detection method, in contrast to fluorescent or colorimetric methodologies. Over recent years, solid-phase extraction–based techniques, such as the Agilent RapidFire system, have emerged that are capable of analyzing samples in <10 s. While dramatically faster than liquid chromatography–coupled MS, an analysis time of 8–10 s is still considered relatively slow for full-diversity high-throughput screening (HTS). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) offers an alternative for high-throughput MS detection. However, sample preparation and deposition onto the MALDI target, as well as interference from matrix ions, have been considered limitations for the use of MALDI for screening assays. Here we describe the development and validation of assays for both small-molecule and peptide analytes using MALDI-TOF coupled with nanoliter liquid handling. Using the JMJD2c histone demethylase and acetylcholinesterase as model systems, we have generated robust data in a 1536 format and also increased sample deposition to 6144 samples per target. Using these methods, we demonstrate that this technology can deliver fast sample analysis time with low sample volume, and data comparable to that of current RapidFire assays.
Collapse
Affiliation(s)
- Carl Haslam
- Department of Biological Sciences, GlaxoSmithKline, Stevenage, UK
| | - John Hellicar
- Department of Biological Sciences, GlaxoSmithKline, Stevenage, UK
| | - Adrian Dunn
- Department of Chemical Sciences, GlaxoSmithKline, Stevenage, UK
| | | | - Neil Hardy
- Department of Sample Management and Automation, GlaxoSmithKline, Stevenage, UK
| | - Peter Marshall
- Department of Chemical Sciences, GlaxoSmithKline, Stevenage, UK
| | | | | | | | | |
Collapse
|
19
|
Richardson SL, Hanjra P, Zhang G, Mackie BD, Peterson DL, Huang R. A direct, ratiometric, and quantitative MALDI-MS assay for protein methyltransferases and acetyltransferases. Anal Biochem 2015; 478:59-64. [PMID: 25778392 DOI: 10.1016/j.ab.2015.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/18/2015] [Accepted: 03/04/2015] [Indexed: 01/22/2023]
Abstract
Protein methylation and acetylation play important roles in biological processes, and misregulation of these modifications is involved in various diseases. Therefore, it is critical to understand the activities of the enzymes responsible for these modifications. Herein we describe a sensitive method for ratiometric quantification of methylated and acetylated peptides via MALDI-MS by direct spotting of enzymatic methylation and acetylation reaction mixtures without tedious purification procedures. The quantifiable detection limit for peptides with our method is approximately 10 fmol. This is achieved by increasing the signal-to-noise ratio through the addition of NH4H2PO4 to the matrix solution and reduction of the matrix α-cyanohydroxycinnamic acid concentration to 2 mg/ml. We have demonstrated the application of this method in enzyme kinetic analysis and inhibition studies. The unique feature of this method is the simultaneous quantification of multiple peptide species for investigation of processivity mechanisms. Its wide buffer compatibility makes it possible to be adapted to investigate the activity of any protein methyltransferase or acetyltransferase.
Collapse
Affiliation(s)
- Stacie L Richardson
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Pahul Hanjra
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Gang Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Brianna D Mackie
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Darrell L Peterson
- Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA; Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Rong Huang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA.
| |
Collapse
|
20
|
de Rond T, Danielewicz M, Northen T. High throughput screening of enzyme activity with mass spectrometry imaging. Curr Opin Biotechnol 2014; 31:1-9. [PMID: 25129648 DOI: 10.1016/j.copbio.2014.07.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 07/29/2014] [Accepted: 07/29/2014] [Indexed: 10/24/2022]
Abstract
Mass spectrometry imaging (MSI) has found a diversity of applications ranging from localizing metabolites and proteins in tissues to investigating microbial interactions, and as a result is perhaps the fastest growing subfield of mass spectrometry. Advances in surface mass spectrometry technologies are equally applicable to the analysis of arrayed samples. One promising field in which this capacity has been leveraged is the high-throughput analysis of enzyme activity, an important step in the development of a wide range of biotechnologies. This review article describes several emerging approaches that seek to improve the quality and scope of this application of MSI.
Collapse
Affiliation(s)
- Tristan de Rond
- Dept. of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Megan Danielewicz
- Lawrence Berkeley National Lab, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Trent Northen
- Lawrence Berkeley National Lab, One Cyclotron Road, Berkeley, CA 94720, USA; Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.
| |
Collapse
|
21
|
Guitot K, Scarabelli S, Drujon T, Bolbach G, Amoura M, Burlina F, Jeltsch A, Sagan S, Guianvarc’h D. Label-free measurement of histone lysine methyltransferases activity by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 2014; 456:25-31. [DOI: 10.1016/j.ab.2014.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 11/28/2022]
|
22
|
Direct MALDI-TOF/TOF analyses of unnatural beauvericins produced by the endophytic fungus Fusarium oxysporum SS46. REVISTA BRASILEIRA DE FARMACOGNOSIA 2014. [DOI: 10.1016/j.bjp.2014.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
23
|
Gode D, Schmitt C, Engel M, Volmer DA. Screening Dyrk1A inhibitors by MALDI-QqQ mass spectrometry: systematic comparison to established radiometric, luminescence, and LC-UV-MS assays. Anal Bioanal Chem 2014; 406:2841-52. [PMID: 24618988 DOI: 10.1007/s00216-014-7703-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/12/2014] [Accepted: 02/17/2014] [Indexed: 11/26/2022]
Abstract
Enzyme-catalyzed reactions play key roles in disease pathology, thus making them relevant subjects of therapeutic inhibitor screening experiments. Matrix-assisted laser desorption/ionization (MALDI) assays have been demonstrated to be able to replace established screening approaches. They offer increased sample throughput, but care must be taken to avoid instrumental bias from differences in ionization efficiencies. We compared a MALDI-triple-quadrupole (QqQ) method for the Dyrk1A peptide substrate woodtide to LC-MS, liquid chromatography with ultraviolet detection (LC-UV), luminescence, and radiometric assays. MALDI measurements were performed on a MALDI-QqQ instrument in the multiple-reaction monitoring mode. Different MALDI conditions were investigated to address whether matrix type, sample support, and MRM- or SIM-based detection conditions can be used to accommodate the molar responses of substrate peptide and its phosphorylated form. UV detection served as a reference method. The impact of MALDI matrix on IC50 values was small, even considering that matrix preparations were used that are known to alleviate response differences. IC50 values determined by MALDI were ca. 2-fold lower than those determined by LC-UV. Although MALDI generated lower ion yields for the phosphorylated peptide than for the peptide substrate, we found that a correction of compound potencies was readily possible using correction factors based on unbiased LC-UV results. A thorough method development delivered a robust assay with excellent performance (Z' > 0.91) that was close to that seen for LC-UV.
Collapse
Affiliation(s)
- David Gode
- Institute of Bioanalytical Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | | | | | | |
Collapse
|
24
|
Development and validation of an indirect pulsed electrochemical detection method for monitoring the inhibition of Abl1 tyrosine kinase. J Pharm Biomed Anal 2014; 90:52-7. [DOI: 10.1016/j.jpba.2013.11.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/15/2013] [Accepted: 11/17/2013] [Indexed: 01/02/2023]
|
25
|
Li J, Lipson RH. Assays Using a NIMS Chip: Loosely Bound but Highly Selective. Anal Chem 2013; 85:6860-5. [DOI: 10.1021/ac401101j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- J. Li
- Department of Chemistry, University of Victoria, P.O. Box 3065,
Stn CSC, Victoria BC V8W 3V6, Canada
| | - R. H. Lipson
- Department of Chemistry, University of Victoria, P.O. Box 3065,
Stn CSC, Victoria BC V8W 3V6, Canada
| |
Collapse
|
26
|
Zhou J, Xu X, Liu W, Liu X, Nie Z, Qing M, Nie L, Yao S. Graphene oxide-peptide nanocomplex as a versatile fluorescence probe of protein kinase activity based on phosphorylation protection against carboxypeptidase digestion. Anal Chem 2013; 85:5746-54. [PMID: 23734972 DOI: 10.1021/ac400336u] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The research on complicated kinomics and kinase-target drug discovery requires the development of simple, cost-effective, and multiplex kinase assays. Herein, we propose a novel and versatile biosensing platform for the detection of protein kinase activity based on graphene oxide (GO)-peptide nanocomplex and phosphorylation-induced suppression of carboxypeptidase Y (CPY) cleavage. Kinase-catalyzed phosphorylation protects the fluorophore-labeled peptide probe against CPY digestion and induces the formation of a GO/peptide nanocomplex resulting in fluorescence quenching, while the nonphosphopeptide is degraded by CPY to release free fluorophore as well as restore fluorescence. This GO-based nanosensor has been successfully applied to sensitively detect two model kinases, casein kinase (CKII) and cAMP-dependent protein kinase (PKA) with low detection limits of 0.0833 mU/μL and 0.134 mU/μL, respectively. The feasibility of this GO-based sensor was further demonstrated by the assessment of kinase inhibition by staurosporine and H-89, in vitro kinase assay in cell lysates, and simultaneous detection of CKII and PKA activity. Moreover, the GO-based fluorescence anisotropy (FA) kinase assay has been also developed using GO as a FA signal amplifier. The proposed sensor is homogeneous, facile, universal, label-free, and applicable for multiplexed kinase assay, presenting a promising method for kinase-related biochemical fundamental research and inhibitor screening.
Collapse
Affiliation(s)
- Jiang Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Chen H, Adams E, Van Schepdael A. LC-ESI-MS method for the monitoring of Abl 1 tyrosine kinase. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 897:17-21. [PMID: 22538123 DOI: 10.1016/j.jchromb.2012.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 03/21/2012] [Accepted: 04/02/2012] [Indexed: 10/28/2022]
Abstract
A liquid chromatography-electrospray ionization-mass spectrometric (LC-ESI-MS) method was developed and validated to study Abl 1 tyrosine kinase. An online desalting system was adopted, and a transformation of the ratio of product to substrate instead of a deuterated internal standard was introduced to calculate the concentration of product. In this study, the substrate used was Abltide (KKGEAIYAAPFA-NH₂). The detection was performed by selected ion monitoring (SIM) mode via positive ESI interface. Chromatographic separation was achieved on a C₁₈ column using an isocratic mobile phase system. The limit of quantification (LOQ) was 10nM for the product and 25 nM for the substrate. The simple ratios of product to substrate maintained a linear relationship (R²=0.9997) over the ratio of 0-50% product. Intra- and inter-day precision was less than 10% and accuracy was from -1.6 to +5.3%. The validated method was applied to the Abl 1 kinase kinetic study and the K(m) and V(max) constants obtained for Abltide were 34.78 μM and 5.563 μmol/mg/min and for adenosine triphosphate (ATP) were 43.61 μM and 5.906 μmol/mg/min. The enzymatic reaction of Abl 1 tyrosine kinase belongs to ternary-complex mechanism.
Collapse
Affiliation(s)
- Hui Chen
- Laboratory for Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Katholieke Universiteit Leuven, O&N 2, PB 923, Herestraat 49, B-3000 Leuven, Belgium
| | | | | |
Collapse
|
28
|
Ji L, Wu JH, Luo Q, Li X, Zheng W, Zhai G, Wang F, Lü S, Feng YQ, Liu J, Xiong S. Quantitative mass spectrometry combined with separation and enrichment of phosphopeptides by titania coated magnetic mesoporous silica microspheres for screening of protein kinase inhibitors. Anal Chem 2012; 84:2284-91. [PMID: 22304342 DOI: 10.1021/ac202897u] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We describe herein the development of a matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF-MS) approach for screening of protein kinase inhibitors (PKIs). MS quantification of phosphopeptides, the kinase-catalyzed products of nonphosphorylated substrates, is a great challenge due to the ion suppression effect of highly abundant nonphosphorylated peptides in enzymatic reaction mixtures. To address this issue, a novel type of titania coated magnetic hollow mesoporous silica spheres (TiO(2)/MHMSS) material was fabricated for capturing phosphopeptides from the enzymatic reaction mixtures prior to MS analysis. Under optimized conditions, even in the presence of 1000-fold of a substrate peptide of tyrosine kinase epidermal growth factor receptor (EGFR), the phosphorylated substrates at the femtomole level can be detected with high accuracy and reproducibility. With a synthetic nonisotopic labeled phosphopeptide, of which the sequence is similar to that of the phosphorylated substrate, as the internal standard, the MS signal ratio of the phosphorylated substrate to the standard is linearly correlated with the molar ratio of the two phosphopeptides in peptide mixtures over the range of 0.1 to 4 with r(2) being 0.99. The IC(50) values of three EGFR inhibitors synthesized in our laboratory were then determined, and the results are consistent with those determined by an enzyme-linked immunosorbent assay (ELISA). The developed method is sensitive, cost/time-effective, and operationally simple and does not require isotope/radioative-labeling, providing an ideal alterative for screening of PKIs as therapeutic agents.
Collapse
Affiliation(s)
- Liyun Ji
- Beijing National Laboratory for Molecular Sciences, Beijing Centre for Mass Spectrometry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Yin P, Bousquet-Moore D, Annangudi SP, Southey BR, Mains RE, Eipper BA, Sweedler JV. Probing the production of amidated peptides following genetic and dietary copper manipulations. PLoS One 2011; 6:e28679. [PMID: 22194882 PMCID: PMC3241674 DOI: 10.1371/journal.pone.0028679] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 11/13/2011] [Indexed: 11/23/2022] Open
Abstract
Amidated neuropeptides play essential roles throughout the nervous and endocrine systems. Mice lacking peptidylglycine α-amidating monooxygenase (PAM), the only enzyme capable of producing amidated peptides, are not viable. In the amidation reaction, the reactant (glycine-extended peptide) is converted into a reaction intermediate (hydroxyglycine-extended peptide) by the copper-dependent peptidylglycine-α-hydroxylating monooxygenase (PHM) domain of PAM. The hydroxyglycine-extended peptide is then converted into amidated product by the peptidyl-α-hydroxyglycine α-amidating lyase (PAL) domain of PAM. PHM and PAL are stitched together in vertebrates, but separated in some invertebrates such as Drosophila and Hydra. In addition to its luminal catalytic domains, PAM includes a cytosolic domain that can enter the nucleus following release from the membrane by γ-secretase. In this work, several glycine- and hydroxyglycine-extended peptides as well as amidated peptides were qualitatively and quantitatively assessed from pituitaries of wild-type mice and mice with a single copy of the Pam gene (PAM+/−) via liquid chromatography-mass spectrometry-based methods. We provide the first evidence for the presence of a peptidyl-α-hydroxyglycine in vivo, indicating that the reaction intermediate becomes free and is not handed directly from PHM to PAL in vertebrates. Wild-type mice fed a copper deficient diet and PAM+/− mice exhibit similar behavioral deficits. While glycine-extended reaction intermediates accumulated in the PAM+/− mice and reflected dietary copper availability, amidated products were far more prevalent under the conditions examined, suggesting that the behavioral deficits observed do not simply reflect a lack of amidated peptides.
Collapse
Affiliation(s)
- Ping Yin
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Danielle Bousquet-Moore
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Suresh P. Annangudi
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Bruce R. Southey
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Richard E. Mains
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Betty A. Eipper
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut, United States of America
- * E-mail: (JVS); (BAE)
| | - Jonathan V. Sweedler
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (JVS); (BAE)
| |
Collapse
|
30
|
Urban PL, Schmidt AM, Fagerer SR, Amantonico A, Ibañez A, Jefimovs K, Heinemann M, Zenobi R. Carbon-13 labelling strategy for studying the ATP metabolism in individual yeast cells by micro-arrays for mass spectrometry. MOLECULAR BIOSYSTEMS 2011; 7:2837-40. [PMID: 21850345 DOI: 10.1039/c1mb05248a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Isotopic labelling of cellular metabolites, used in conjunction with high-density micro-arrays for mass spectrometry enables observation of ATP metabolism in single yeast cells.
Collapse
Affiliation(s)
- Pawel L Urban
- Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Urban PL, Amantonico A, Zenobi R. Lab-on-a-plate: extending the functionality of MALDI-MS and LDI-MS targets. MASS SPECTROMETRY REVIEWS 2011; 30:435-478. [PMID: 21254192 DOI: 10.1002/mas.20288] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We review the literature that describes how (matrix-assisted) laser desorption/ionization (MA)LDI target plates can be used not only as sample supports, but beyond that: as functional parts of analytical protocols that incorporate detection by MALDI-MS or matrix-free LDI-MS. Numerous steps of analytical procedures can be performed directly on the (MA)LDI target plates prior to the ionization of analytes in the ion source of a mass spectrometer. These include homogenization, preconcentration, amplification, purification, extraction, digestion, derivatization, synthesis, separation, detection with complementary techniques, data storage, or other steps. Therefore, we consider it helpful to define the "lab-on-a-plate" as a format for carrying out extensive sample treatment as well as bioassays directly on (MA)LDI target plates. This review introduces the lab-on-plate approach and illustrates it with the aid of relevant examples from the scientific and patent literature.
Collapse
Affiliation(s)
- Pawel L Urban
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | | | | |
Collapse
|
32
|
Touati J, Angelini A, Hinner MJ, Heinis C. Enzymatic cyclisation of peptides with a transglutaminase. Chembiochem 2011; 12:38-42. [PMID: 21154802 DOI: 10.1002/cbic.201000451] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jeremy Touati
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | | | | |
Collapse
|
33
|
Djung JF, Mears RJ, Montalbetti CA, Coulter TS, Golebiowski A, Carr AN, Barker O, Greis KD, Zhou S, Dolan E, Davis GF. The synthesis and evaluation of indolylureas as PKCα inhibitors. Bioorg Med Chem 2011; 19:2742-50. [DOI: 10.1016/j.bmc.2011.02.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Revised: 02/17/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
|
34
|
Zhou G, Sylvester JE, Wu D, Veach DR, Kron SJ. A magnetic bead-based protein kinase assay with dual detection techniques. Anal Biochem 2010; 408:5-11. [PMID: 20807497 DOI: 10.1016/j.ab.2010.08.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 08/17/2010] [Accepted: 08/26/2010] [Indexed: 01/08/2023]
Abstract
A novel magnetic bead-based protein kinase assay was developed using MALDI-TOF mass spectrometry (MALDI-TOF MS) and immunochemifluorescence as two independent detection techniques. Abltide substrate was immobilized onto magnetic beads via noncovalent biotin-streptavidin interactions. This noncovalent immobilization strategy facilitated peptide release and allowed MALDI-TOF MS analysis of substrate phosphorylation. The use of magnetic beads provided rapid sample handling and allowed secondary analysis by immunochemifluorescence to determine the degree of substrate phosphorylation. This dual detection technique was used to evaluate the inhibition of c-Abl kinase by imatinib and dasatinib. For each inhibitor, IC₅₀ (half-maximal inhibitory concentration) values determined by these two different detection methods were consistent and close to values reported in the literature. The high-throughput potential of this new approach to kinase assays was preliminarily demonstrated by screening a chemical library consisting of 31 compounds against c-Abl kinase using a 96-well plate. In this proof-of-principle experiment, both MALDI-TOF MS and immunochemifluorescence were able to compare inhibitor potencies with consistent values. Dual detection may significantly enhance the reliability of chemical library screening and identify false positives and negatives. Formatted for 96-well plates and with high-throughput potential, this dual detection kinase assay may provide a rapid, reliable, and inexpensive route to the discovery of small-molecule drug leads.
Collapse
Affiliation(s)
- Guangchang Zhou
- Ludwig Center for Metastasis Research, The University of Chicago, IL 60637, USA
| | | | | | | | | |
Collapse
|
35
|
Zhang D, Huang W, Dai B, Zhao T, Ashraf A, Millard RW, Ashraf M, Wang Y. Genetically manipulated progenitor cell sheet with diprotin A improves myocardial function and repair of infarcted hearts. Am J Physiol Heart Circ Physiol 2010; 299:H1339-47. [PMID: 20802132 DOI: 10.1152/ajpheart.00592.2010] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We postulated that the combination of overexpression of CXCR4 in mesenchymal stem cells (MSC) with diprotin A would enhance MSC recruitment and penetration into ischemic myocardium, leading to an improvement in heart function after myocardial infarction (MI). Male rat MSC were genetically engineered with adenoviral vectors coexpressing CXCR4 and enhanced green fluorescent protein (EGFP) (MSC(CXCR4)), GFP alone (MSC(Null), control), or siRNA-targeted CXCR4 (MSC(siRNA)). Cell sheets were applied over the surface of infarcted left ventricle (LV) in female rats 7 days after ligation of the left anterior descending coronary artery (LAD) pretreated with either vehicle (VEH) or diprotin A (DIP). At 28 days after cell sheet implantation, echocardiography was performed. Hearts were harvested for histological analysis 7 days after LAD ligation or 28 days after cell sheet implantation. DPP-IV and stroma-derived factor-1α (SDF-1α) in the LV were analyzed. Efficacy of engraftment was determined by the presence of Y chromosome in nuclei (Y(ch+)). LV blood vessel density and apoptosis were also analyzed. Myocardial SDF-1α was elevated before placement of the cell sheet in the DIP group compared with vehicle group on day 7 after LAD. On day 28 after cell sheet transplantation, the number of Y(ch+) was increased in the MSC(CXCR4) + VEH group compared with the MSC(Null) + VEH group and further increased in the MSC(CXCR4) + DIP treated group. This enhanced response was associated with increased angiogenesis in both sides of epicardium and improvement of LV function. Combination of gene-manipulated MSC(CXCR4) patch with DIP pretreatment inhibits myocardial ischemia-induced apoptosis, promotes tissue angiogenesis, and enhances cell engraftment, leading to improved LV mechanical function after MI.
Collapse
Affiliation(s)
- Dongsheng Zhang
- Department of Pathology and Laboratory Medicine, University of Cincinnati Medical Center, Cincinnati, Ohio 45267-0529, USA
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Rathore R, Pribil P, Corr JJ, Seibel WL, Evdokimov A, Greis KD. Multiplex enzyme assays and inhibitor screening by mass spectrometry. ACTA ACUST UNITED AC 2010; 15:1001-7. [PMID: 20228278 DOI: 10.1177/1087057110363824] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Current methods for high-throughput screening (HTS) use a serial process to evaluate compounds as inhibitors toward a single therapeutic target, but as the demand to reduce screening time and cost continues to grow, one solution is the development of multiplex technology. In this communication, the multiplex assay capability of a mass spectrometry (MS)-based readout system is verified using a kinase and esterase reaction simultaneously. Furthermore, the MS-based readout is shown to be compatible with a typical HTS workflow by identifying and validating several new inhibitors for each enzyme from a small library of compounds. These data confirm that it is possible to monitor inhibition of multiple therapeutic targets with one pass through the compound repository, thus demonstrating the potential for MS-based methods to become a method of choice for HTS of isolated enzymes.
Collapse
Affiliation(s)
- Rakesh Rathore
- Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45237, USA
| | | | | | | | | | | |
Collapse
|
37
|
Lü S, Luo Q, Li X, Wu J, Liu J, Xiong S, Feng YQ, Wang F. Inhibitor screening of protein kinases using MALDI-TOF MS combined with separation and enrichment of phosphopeptides by TiO2 nanoparticle deposited capillary column. Analyst 2010; 135:2858-63. [DOI: 10.1039/c0an00339e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
38
|
Rathore R, Corr JJ, Lebre DT, Seibel WL, Greis KD. Extending matrix-assisted laser desorption/ionization triple quadrupole mass spectrometry enzyme screening assays to targets with small molecule substrates. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:3293-3300. [PMID: 19757451 DOI: 10.1002/rcm.4248] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Mass spectrometry (MS)-based high-throughput screening (HTS) has tremendous potential as an alternative to current screening methods due to its speed, sensitivity, reproducibility and label-free readout. We recently reported that a new generation matrix-assisted laser desorption/ionization triple quadrupole (MALDI-QqQ) mass spectrometer is ideally suited for a variety of enzyme assays and screening protocols. However, all the targets measured to date had peptide substrates that were easily monitored by selected ion monitoring (SIM) without interference from the MALDI matrix. To further extend the application to enzymes with small molecule, non-peptide substrates, we evaluated this method for measuring enzyme activity and inhibition of acetylcholinesterase (AChE). Due to the potential of MALDI matrix interference, multiple reaction monitoring (MRM) was investigated for selective MS/MS transitions and to accurately measure the conversion of acetylcholine into choline. Importantly, ionization, detection and MRM transition efficiency differences between the substrate and product can be overcome by pre-balancing the MRM transitions during method development, thus allowing for a direct readout of the enzyme activity using the ratio of the substrate and product signals. Further validation of the assay showed accurate concentration-dependent inhibition measurements of AChE with several known inhibitors. Finally, a small library of 1008 drug-like compounds was screened at a single dose (10 microM) and the top 10 inhibitors from this primary screen were validated in a secondary screen to determine the rank order of inhibitory potency for each compound. Collectively, these data demonstrate that a MALDI-QqQMS-based readout platform is amenable to measuring small molecule substrates and products and offers significant advantages over current HTS methods in terms of speed, sensitivity, reproducibility and reagent costs.
Collapse
Affiliation(s)
- Rakesh Rathore
- Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45237, USA
| | | | | | | | | |
Collapse
|
39
|
Rathore R, Corr J, Scott G, Vollmerhaus P, Greis KD. Development of an inhibitor screening platform via mass spectrometry. ACTA ACUST UNITED AC 2008; 13:1007-13. [PMID: 19029013 DOI: 10.1177/1087057108326143] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Commonly used methods for isolated enzyme inhibitor screening typically rely on fluorescent or chemiluminescent detection techniques that are often indirect and/or coupled assays. Mass spectrometry (MS) has been widely reported for measuring the conversion of substrates to products for enzyme assays and has more recently been demonstrated as an alternative readout system for inhibitor screening. In this report, a high-throughput mass spectrometry (HTMS) readout platform, based on the direct measurement of substrate conversion to product, is presented. The rapid ionization and desorption features of a new generation matrix-assisted laser desorption ionization-triple quadrupole (MALDI-QqQ) mass spectrometer are shown to improve the speed of analysis to greater than 1 sample per second while maintaining excellent Z' values. Furthermore, the readout was validated by demonstrating the ability to measure IC(50) values for several known kinase inhibitors against cyclic AMP-dependent protein kinase (PKA). Finally, when the assay performance was compared with a common ADP accumulation readout system, this HTMS approach produced better signal-to-background ratios, higher Z' values, and a reagent cost of about $0.03 per well compared with about $0.60 per well for the fluorescence assay. Collectively, these data demonstrate that a MALDI-QqQ-MS-based readout platform offers significant advantages over the commonly used assays in terms of speed, sensitivity, reproducibility, and reagent cost.
Collapse
Affiliation(s)
- Rakesh Rathore
- University of Cincinnati, Department of Cancer and Cell Biology, Cincinnati, OH, USA
| | | | | | | | | |
Collapse
|
40
|
Winkle RF, Nagy JM, Cass AEG, Sharma S. Towards microfluidic technology-based MALDI-MS platforms for drug discovery: a review. Expert Opin Drug Discov 2008; 3:1281-92. [DOI: 10.1517/17460441.3.11.1281] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
41
|
Hollemeyer K, Altmeyer W, Heinzle E, Pitra C. Species identification of Oetzi's clothing with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry based on peptide pattern similarities of hair digests. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:2751-2767. [PMID: 18720427 DOI: 10.1002/rcm.3679] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Identification of ancient biological samples from the 1991-discovered and more than 5300-year-old Tyrolean mummy, also called iceman or Oetzi, is very difficult. The species of origins of four animal-hair-bearing samples of the accoutrement of the mummy not yet diagnosed were identified by a special proteomics method. Ha 43/91/130 and Ha 6/91, two samples from his coat, and Ha 5/91, a sample from his leggings, were assigned to sheep. The upper leather of his moccasins, Ha 2/91, was made from cattle. Despite the enormous age of these samples with partial (bio)chemical alterations, reliable identification was possible using a recently developed matrix-assisted laser desorption/ionization time-of-flight mass spectrometric ((MALDI-TOF MS)-based analytical method. The method is exclusively based on the analysis of proteins and uses minute amounts of peptides directly derived from tryptic hair digests without any separation or enrichment steps. Unknown species are identified by comparison of their peptide ion patterns with known spectra stored in existing databases. Hereby, the correlation distance, a form of Euclidean distance, and deduced parameters are used to measure similarities. If more than one potential hit remains, specific diagnostic peptide ions are used to stepwise exclude incorrect matches. These ions are specific for orders, families, subfamilies/genera and/or even species. Peptide mass fingerprinting data combined with those from collision-induced dissociation spectra (combined MS & MS/MS) were used for interpretation with the MASCOT search engine and the NCBI database to find the potential parentage of hair proteins. For this technique, selected precursor ions were identified as specific diagnostic peptide ions.
Collapse
Affiliation(s)
- Klaus Hollemeyer
- Biochemical Engineering Institute, Saarland University, Saarbruecken, Germany.
| | | | | | | |
Collapse
|
42
|
|
43
|
Affinity selection-mass spectrometry screening techniques for small molecule drug discovery. Curr Opin Chem Biol 2007; 11:518-26. [PMID: 17931956 DOI: 10.1016/j.cbpa.2007.07.011] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 07/21/2007] [Accepted: 07/27/2007] [Indexed: 11/24/2022]
|
44
|
de Boer AR, Lingeman H, Niessen WM, Irth H. Mass spectrometry-based biochemical assays for enzyme-inhibitor screening. Trends Analyt Chem 2007. [DOI: 10.1016/j.trac.2007.08.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
45
|
Vogel M, Scheffer A, Liesener A, Karst U. Laser Desorption Assays – MALDI‐MS, DIOS‐MS, and SAMDI‐MS. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/9783527610907.ch8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
46
|
Greis KD. Mass spectrometry for enzyme assays and inhibitor screening: an emerging application in pharmaceutical research. MASS SPECTROMETRY REVIEWS 2007; 26:324-39. [PMID: 17405133 DOI: 10.1002/mas.20127] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Robust methods that monitor enzyme activity and inhibitor potency are crucial to drug discovery and development. Over the past 20 years, mass spectrometric methods have increasingly been used to measure enzyme activity and kinetics. However, for rapid screening of inhibitory compounds, various forms of fluorescence and chemiluminscence readout have continued to dominate the market. As the sensitivity, speed, and miniaturization of mass spectrometry methods continue to advance, opportunities to couple mass spectrometry with screening will continue to come to the forefront. To appreciate the tremendous potential for MS-based screening assays, it becomes necessary to understand the current state of capabilities in this arena. Thus, this review is intended to capture how mass spectrometry for studying enzymes activity has progressed from simple qualitative questions (i.e., is the product detected?) to quantitative measures of enzyme activity and kinetics and then as a tool for rapidly screening inhibitory compounds as an alternative to current methods of high throughput drug screening.
Collapse
Affiliation(s)
- Kenneth D Greis
- Genome Research Institute, University of Cincinnati, 2180 E. Galbraith Road, Cincinnati, Ohio 45237, USA.
| |
Collapse
|
47
|
Abstract
The rate of drug discovery is greatly dependent on the development and improvement of rapid and reliable analytical methods that allow screening for protein-ligand interactions. The solution-based methods for investigating protein-ligand interactions by mass spectrometry (MS), which are discussed in this paper, are hydrogen/deuterium exchange of protein backbone amide hydrogens, and photoaffinity labeling. Moreover, MS analysis of intact noncovalent protein-ligand complexes is described. Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) with its ultra-high resolution and excellent mass accuracy is also considered herein as it is gaining increasing popularity for a mass spectrometric investigation of protein-ligand interactions.
Collapse
Affiliation(s)
- Andrea Sinz
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle, Germany.
| |
Collapse
|
48
|
Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:407-418. [PMID: 17326037 DOI: 10.1002/jms.1072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
|
49
|
Pastwa E, Somiari SB, Czyz M, Somiari RI. Proteomics in human cancer research. Proteomics Clin Appl 2006; 1:4-17. [PMID: 21136608 DOI: 10.1002/prca.200600369] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Indexed: 01/07/2023]
Abstract
Proteomics is now widely employed in the study of cancer. Many laboratories are applying the rapidly emerging technologies to elucidate the underlying mechanisms associated with cancer development, progression, and severity in addition to developing drugs and identifying patients who will benefit most from molecular targeted compounds. Various proteomic approaches are now available for protein separation and identification, and for characterization of the function and structure of candidate proteins. In spite of significant challenges that still exist, proteomics has rapidly expanded to include the discovery of novel biomarkers for early detection, diagnosis and prognostication (clinical application), and for the identification of novel drug targets (pharmaceutical application). To achieve these goals, several innovative technologies including 2-D-difference gel electrophoresis, SELDI, multidimensional protein identification technology, isotope-coded affinity tag, solid-state and suspension protein array technologies, X-ray crystallography, NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulation have evolved, and are being used in different combinations. This review provides an overview of the field of proteomics and discusses the key proteomic technologies available to researchers. It also describes some of the important challenges and highlights the current pharmaceutical and clinical applications of proteomics in human cancer research.
Collapse
Affiliation(s)
- Elzbieta Pastwa
- Molecular Genetics Department, Medical University of Lodz, Lodz, Poland.
| | | | | | | |
Collapse
|
50
|
Warshakoon NC, Wu S, Boyer A, Kawamoto R, Sheville J, Renock S, Xu K, Pokross M, Zhou S, Winter C, Walter R, Mekel M, Evdokimov AG. Structure-based design, synthesis, and SAR evaluation of a new series of 8-hydroxyquinolines as HIF-1α prolyl hydroxylase inhibitors. Bioorg Med Chem Lett 2006; 16:5517-22. [PMID: 16931007 DOI: 10.1016/j.bmcl.2006.08.040] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 08/07/2006] [Accepted: 08/08/2006] [Indexed: 11/29/2022]
Abstract
A new series of potent 8-hydroxyquinolines was designed based on the newly resolved X-ray crystal structure of EGLN-1. Both alkyl and aryl 8-hydroxyquinoline-7-carboxyamides were good HIF-1alpha prolyl hydroxylase (EGLN) inhibitors. In subsequent VEGF induction assays, these exhibited potent VEGF activity. In addition, this class of compounds did show the ability to stabilize HIF-1alpha.
Collapse
Affiliation(s)
- Namal C Warshakoon
- Drug Discovery Division, Procter and Gamble Pharmaceuticals Inc., 8700 Mason-Montgomery Road, Mason, OH 45040, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|