1
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Phan M, Chandrashekaran IR, Akhtar N, Konstantinidou E, Devine SM, Doak BC, Nebl T, Creek DJ, Scanlon MJ, Norton RS. Multiplexed Native Mass Spectrometry Determination of Ligand Selectivity for Fatty Acid-Binding Proteins. ACS Med Chem Lett 2024; 15:1071-1079. [PMID: 39015264 PMCID: PMC11247632 DOI: 10.1021/acsmedchemlett.4c00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 07/18/2024] Open
Abstract
Although multiple approaches for characterizing protein-ligand interactions are available in target-based drug discovery, their throughput for determining selectivity is quite limited. Herein, we describe the application of native mass spectrometry for rapid, multiplexed screening of the selectivity of eight small-molecule ligands for five fatty acid-binding protein isoforms. Using high-resolution mass spectrometry, we were able to identify and quantify up to 20 different protein species in a single spectrum. We show that selectivity profiles generated by native mass spectrometry are in good agreement with those of traditional solution-phase techniques such as isothermal titration calorimetry and fluorescence polarization. Furthermore, we propose strategies for effective investigation of selectivity by native mass spectrometry, thus highlighting the potential of this technique to be used as an orthogonal method to traditional biophysical approaches for rapid, multiplexed screening of protein-ligand complexes.
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Affiliation(s)
- Michelle
Q. Phan
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Indu R. Chandrashekaran
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Naureen Akhtar
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Evgenia Konstantinidou
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Shane M. Devine
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Bradley C. Doak
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Thomas Nebl
- Biologics
Research and Development Group, Biomedical Manufacturing Program, CSIRO, Clayton, Victoria 3168, Australia
| | - Darren J. Creek
- Drug
Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Martin J. Scanlon
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Raymond S. Norton
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
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2
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Kaeslin J, Brunner C, Ghiasikhou S, Schneider G, Zenobi R. Bioaffinity Screening with a Rapid and Sample-Efficient Autosampler for Native Electrospray Ionization Mass Spectrometry. Anal Chem 2021; 93:13342-13350. [PMID: 34546705 DOI: 10.1021/acs.analchem.1c03130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fast and efficient handling of ligands and biological targets are required in bioaffinity screening based on native electrospray ionization mass spectrometry (ESI-MS). We use a prototype microfluidic autosampler, called the "gap sampler", to sequentially mix and electrospray individual small molecule ligands together with a target protein and compare the screening results with data from thermal shift assay and surface plasmon resonance. In a first round, all three techniques were used for a screening of 110 ligands against bovine carbonic anhydrase II, which resulted in five mutual hits and some false positives with ESI-MS presumably due to the high ligand concentration or interferences from dimethyl sulfoxide. In a second round, 33 compounds were screened in lower concentrations and in a less complex matrix, resulting in only true positives with ESI-MS. Within a cycle time of 30 s, dissociation constants were determined within an order of magnitude accuracy consuming only 5 pmol of ligand and less than 15 pmol of protein per screened compound. In a third round, dissociation constants of five compounds were accurately determined in a titration experiment. Thus, the gap sampler can rapidly and efficiently be used for high-throughput screening.
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Affiliation(s)
- Jérôme Kaeslin
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Cyrill Brunner
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Sahar Ghiasikhou
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
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3
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Ren C, Bailey AO, VanderPorten E, Oh A, Phung W, Mulvihill MM, Harris SF, Liu Y, Han G, Sandoval W. Quantitative Determination of Protein–Ligand Affinity by Size Exclusion Chromatography Directly Coupled to High-Resolution Native Mass Spectrometry. Anal Chem 2018; 91:903-911. [DOI: 10.1021/acs.analchem.8b03829] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Aaron O. Bailey
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
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5
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MS methods to study macromolecule-ligand interaction: Applications in drug discovery. Methods 2018; 144:152-174. [PMID: 29890284 DOI: 10.1016/j.ymeth.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022] Open
Abstract
The interaction of small compounds (i.e. ligands) with macromolecules or macromolecule assemblies (i.e. targets) is the mechanism of action of most of the drugs available today. Mass spectrometry is a popular technique for the interrogation of macromolecule-ligand interactions and therefore is also widely used in drug discovery and development. Thanks to its versatility, mass spectrometry is used for multiple purposes such as biomarker screening, identification of the mechanism of action, ligand structure optimization or toxicity assessment. The evolution and automation of the instruments now allows the development of high throughput methods with high sensitivity and a minimized false discovery rate. Herein, all these approaches are described with a focus on the methods for studying macromolecule-ligand interaction aimed at defining the structure-activity relationships of drug candidates, along with their mechanism of action, metabolism and toxicity.
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6
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Qiao L, Zhong X, Belghith E, Deng Y, Lin TE, Tobolkina E, Liu B, Girault HH. Electrostatic Spray Ionization from 384-Well Microtiter Plates for Mass Spectrometry Analysis-Based Enzyme Assay and Drug Metabolism Screening. Anal Chem 2017; 89:5983-5990. [PMID: 28452215 DOI: 10.1021/acs.analchem.7b00536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have realized the direct ionization of samples from wells of microtiter plates under atmospheric conditions for mass spectrometry analysis without any liquid delivery system or any additional interface. The microtiter plate is a commercially available 384-well plate without any modification, working as a container and an emitter for electrostatic spray ionization of analytes. The approach provides high throughput for the large batches of reactions and both the qualitative and quantitative analysis of a single compound or mixture. The limits of detection in small drug molecules, peptides, and proteins are similar in comparison with standard direct infusion electrospray ionization. The analysis time per well is only seconds. These analytical merits benefit many microtiter plate-based studies, such as combinatorial chemistry and high throughput screening in enzyme assay or drug metabolism. Herein, we illustrate the application in enzyme assay using tyrosine oxidation catalyzed by tyrosinase in the presence or absence of inhibitors. The potential application in drug development is also demonstrated with cytochrome P450-catalyzed metabolic reactions of two drugs in microtiter plates followed with direct ESTASI-MS/MS-based characterization of the metabolism products.
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Affiliation(s)
- Liang Qiao
- Laboratoire d'Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Rue de l'Industrie 17, CH-1951 Sion, Switzerland.,Chemistry Department, Fudan University , 200433 Shanghai, China
| | - Xiaoqin Zhong
- Laboratoire d'Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Rue de l'Industrie 17, CH-1951 Sion, Switzerland
| | - Emna Belghith
- Laboratoire d'Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Rue de l'Industrie 17, CH-1951 Sion, Switzerland
| | - Yan Deng
- Laboratoire d'Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Rue de l'Industrie 17, CH-1951 Sion, Switzerland.,College of Chemistry and Molecular Engineering, Peking University , 100871 Beijing, China
| | - Tzu-En Lin
- Laboratoire d'Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Rue de l'Industrie 17, CH-1951 Sion, Switzerland
| | - Elena Tobolkina
- Laboratoire d'Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Rue de l'Industrie 17, CH-1951 Sion, Switzerland
| | - Baohong Liu
- Chemistry Department, Fudan University , 200433 Shanghai, China
| | - Hubert H Girault
- Laboratoire d'Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Rue de l'Industrie 17, CH-1951 Sion, Switzerland
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7
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Native Mass Spectrometry in Fragment-Based Drug Discovery. Molecules 2016; 21:molecules21080984. [PMID: 27483215 PMCID: PMC6274484 DOI: 10.3390/molecules21080984] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/14/2016] [Accepted: 07/23/2016] [Indexed: 11/17/2022] Open
Abstract
The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.
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8
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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)
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Affiliation(s)
- Chris D Forbes
- Department of Research Technologies, Bayer Pharmaceuticals Corporation, West Haven, CT 06516, USA
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9
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Rohman M, Wingfield J. High-Throughput Screening Using Mass Spectrometry within Drug Discovery. Methods Mol Biol 2016; 1439:47-63. [PMID: 27316987 DOI: 10.1007/978-1-4939-3673-1_3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In order to detect a biochemical analyte with a mass spectrometer (MS) it is necessary to ionize the analyte of interest. The analyte can be ionized by a number of different mechanisms, however, one common method is electrospray ionization (ESI). Droplets of analyte are sprayed through a highly charged field, the droplets pick up charge, and this is transferred to the analyte. High levels of salt in the assay buffer will potentially steal charge from the analyte and suppress the MS signal. In order to avoid this suppression of signal, salt is often removed from the sample prior to injection into the MS. Traditional ESI MS relies on liquid chromatography (LC) to remove the salt and reduce matrix effects, however, this is a lengthy process. Here we describe the use of RapidFire™ coupled to a triple-quadrupole MS for high-throughput screening. This system uses solid-phase extraction to de-salt samples prior to injection, reducing processing time such that a sample is injected into the MS ~every 10 s.
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Affiliation(s)
- Mattias Rohman
- Reagent and Assay Development, AstraZeneca R&D, Mölndal, Sweden.
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10
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Establish an automated flow injection ESI-MS method for the screening of fragment based libraries: Application to Hsp90. Eur J Pharm Sci 2015; 76:83-94. [DOI: 10.1016/j.ejps.2015.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 04/30/2015] [Accepted: 05/03/2015] [Indexed: 02/06/2023]
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11
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Stojko J, Fieulaine S, Petiot-Bécard S, Van Dorsselaer A, Meinnel T, Giglione C, Cianférani S. Ion mobility coupled to native mass spectrometry as a relevant tool to investigate extremely small ligand-induced conformational changes. Analyst 2015; 140:7234-45. [DOI: 10.1039/c5an01311a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Native and ion-mobility mass spectrometry reveal the conformational evolution over time of a peptide deformylase binding different ligands, which is consistent with slow-tight inhibition of the enzyme.
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Affiliation(s)
- Johann Stojko
- BioOrganic Mass Spectrometry Laboratory (LSMBO)
- IPHC
- Université de Strasbourg
- 67087 Strasbourg
- France
| | - Sonia Fieulaine
- Institute for Integrative Biology of the Cell (I2BC)
- CEA
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
| | - Stéphanie Petiot-Bécard
- BioOrganic Mass Spectrometry Laboratory (LSMBO)
- IPHC
- Université de Strasbourg
- 67087 Strasbourg
- France
| | - Alain Van Dorsselaer
- BioOrganic Mass Spectrometry Laboratory (LSMBO)
- IPHC
- Université de Strasbourg
- 67087 Strasbourg
- France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC)
- CEA
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC)
- CEA
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
| | - Sarah Cianférani
- BioOrganic Mass Spectrometry Laboratory (LSMBO)
- IPHC
- Université de Strasbourg
- 67087 Strasbourg
- France
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12
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Maple HJ, Scheibner O, Baumert M, Allen M, Taylor RJ, Garlish RA, Bromirski M, Burnley RJ. Application of the Exactive Plus EMR for automated protein-ligand screening by non-covalent mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:1561-8. [PMID: 24861608 DOI: 10.1002/rcm.6925] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/14/2014] [Accepted: 04/16/2014] [Indexed: 05/12/2023]
Abstract
RATIONALE Non-covalent mass spectrometry (MS) offers considerable potential for protein-ligand screening in drug discovery programmes. However, there are some limitations with the time-of-flight (TOF) instrumentation typically employed that restrict the application of non-covalent MS in industrial laboratories. METHODS An Exactive Plus EMR mass spectrometer was investigated for its ability to characterise non-covalent protein-small molecule interactions. Nano-electrospray ionisation (nanoESI) infusion was achieved with a TriVersa NanoMate. The transport multipole and ion lens voltages, dissociation energies and pressure in the Orbitrap™ were optimised. Native MS was performed, with ligand titrations to judge retention of protein-ligand interactions, serial dilutions of native proteins as an indication of sensitivity, and a heterogeneous protein analysed for spectral resolution. RESULTS Interactions between native proteins and ligands are preserved during analysis on the Exactive Plus EMR, with the binding affinities determined in good agreement with expected values. High spectral resolution allows baseline separation of adduct ions, which should improve the accuracy and limit of detection for measuring ligand interactions. Data are also presented showing baseline resolution of glycoforms of a highly glycosylated protein, allowing binding of a fragment molecule to be detected. CONCLUSIONS The high sensitivity and spectral resolution achievable with the Orbitrap technology confer significant advantages over TOF mass spectrometers, and offer a solution to current limitations regarding throughput, data analysis and sample requirements. A further benefit of improved spectral resolution is the possibility of using heterogeneous protein samples such as glycoproteins for fragment screening. This would significantly expand the scope of applicability of non-covalent MS in the pharmaceutical and other industries.
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Abstract
Native state mass spectrometry (MS) has been recognised as a rapid, sensitive, and high throughput method to directly investigate protein-ligand interactions for some time, however there are few examples reporting this approach as a screening method to identify relevant protein–fragment interactions in fragment-based drug discovery (FBDD). In this paper an overview of native state MS will be presented, highlighting the attractive properties of this method within the context of fragment screening applications. A summary of published examples using MS for fragment screening will be described and reflection on the outlook for the future adoption and implementation of native state MS as a complementary fragment screening method will be presented.
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14
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Maple HJ, Garlish RA, Rigau-Roca L, Porter J, Whitcombe I, Prosser CE, Kennedy J, Henry AJ, Taylor RJ, Crump MP, Crosby J. Automated Protein–Ligand Interaction Screening by Mass Spectrometry. J Med Chem 2012; 55:837-51. [DOI: 10.1021/jm201347k] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hannah J. Maple
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - Rachel A. Garlish
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Laura Rigau-Roca
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - John Porter
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Ian Whitcombe
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | | | - Jeff Kennedy
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Alistair J. Henry
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Richard J. Taylor
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Matthew P. Crump
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - John Crosby
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
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15
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Bergsdorf C, Ottl J. Affinity-based screening techniques: their impact and benefit to increase the number of high quality leads. Expert Opin Drug Discov 2010; 5:1095-107. [DOI: 10.1517/17460441.2010.524641] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christian Bergsdorf
- Novartis Institutes of BioMedical Research, CPC/LFP/LFT, WSJ-88.07.31, CH-4002 Basel, Switzerland ;
| | - Johannes Ottl
- Novartis Institutes of BioMedical Research, CPC/LFP/LFT, WSJ-88.10.03, CH-4002 Basel, Switzerland
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16
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Woodcroft MW, Ellis DA, Rafferty SP, Burns DC, March RE, Stock NL, Trumpour KS, Yee J, Munro K. Experimental characterization of the mechanism of perfluorocarboxylic acids' liver protein bioaccumulation: the key role of the neutral species. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2010; 29:1669-77. [PMID: 20821618 DOI: 10.1002/etc.199] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Perfluorocarboxylic acids (PFCAs) of chain length greater than seven carbon atoms bioconcentrate in the livers of fish. However, a mechanistic cause for the empirically observed increase in the bioconcentration potential of PFCAs as a function of chain length has yet to be determined. To this end, recombinant rat liver fatty acid-binding protein (L-FABP) was purified, and its interaction with PFCAs was characterized in an aqueous system at pH 7.4. Relative binding affinities of L-FABP with PFCAs of carbon chain lengths of five to nine were established fluorimetrically. The energetics, mechanism, and stoichiometry of the interaction of perfluorooctanoic acid (PFOA) with L-FABP were examined further by isothermal titration calorimetry (ITC) and electrospray ionization combined with tandem mass spectrometry (ESI-MS/MS). Perfluorooctanoic acid was shown to bind to L-FABP with an affinity approximately an order of magnitude less than the natural ligand, oleic acid, and to have at least 3:1 PFOA:L-FABP stoichiometry. Two distinct modes of PFOA binding to L-FABP were observed by ESI-MS/MS analysis; in both cases, PFOA binds solely as the neutral species under typical physiological pH and aqueous concentrations of the anion. A comparison of their chemical and physical properties with other well-studied biologically relevant chemicals showed that accumulation of PFCAs in proteins as the neutral species is predictable. For example, the interaction of PFOA with L-FABP is almost identical to that of the acidic ionizing drugs ketolac, ibuprofen, and warfarin that show specificity to protein partitioning with a magnitude that is proportional to the K(OW) (octanol-water partitioning) of the neutral species. The experimental results suggest that routine pharmacochemical models may be applicable to predicting the protein-based bioaccumulation of long-chain PFCAs.
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Affiliation(s)
- Mark W Woodcroft
- Department of Chemistry, Trent University, 1600 West Bank Drive, Peterborough, Ontario K9J 7B8, Canada
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17
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Native MS: an ’ESI‚ way to support structure- and fragment-based drug discovery. Future Med Chem 2010; 2:35-50. [DOI: 10.4155/fmc.09.141] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The success of early drug-discovery programs depends on the adequate combination of complementary and orthogonal technologies allowing hit/lead compounds to be optimized and improve therapeutic activity. Among the available biophysical methods, native MS recently emerged as an efficient method for compound-binding screening. Native MS is a highly sensitive and accurate screening technique. This review provides a description of the general approach and an overview of the possible characterization of ligand-binding properties. How native MS supports structure- and fragment-based drug research will also be discussed, with examples from the literature and internal developments. Native MS shows strong potential for in-depth characterization of ligand-binding properties. It is also a reliable screening technique in drug-discovery processes.
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18
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Waitt GM, Xu R, Wisely GB, Williams JD. Automated in-line gel filtration for native state mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:239-45. [PMID: 17596960 DOI: 10.1016/j.jasms.2007.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Revised: 05/11/2007] [Accepted: 05/16/2007] [Indexed: 05/16/2023]
Abstract
Characterization of protein-ligand complexes by nondenaturing mass spectrometry provides direct evidence of drug-like molecules binding with potential therapeutic targets. Typically, protein-ligand complexes to be analyzed contain buffer salts, detergents, and other additives to enhance protein solubility, all of which make the sample unable to be analyzed directly by electrospray ionization mass spectrometry. This work describes an in-line gel-filtration method that has been automated and optimized. Automation was achieved using commercial HPLC equipment. Gel column parameters that were optimized include: column dimensions, flow rate, packing material type, particle size, and molecular weight cut-off. Under optimal conditions, desalted protein ions are detected 4 min after injection and the analysis is completed in 20 min. The gel column retains good performance even after >200 injections. A demonstration for using the in-line gel-filtration system is shown for monitoring the exchange of fatty acids from the pocket of a nuclear hormone receptor, peroxisome proliferator activator-delta (PPARdelta) with a tool compound. Additional utilities of in-line gel-filtration mass spectrometry system will also be discussed.
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Affiliation(s)
- Greg M Waitt
- Molecular Discovery Research, GlaxoSmithKline, Research Triangle Park, North Carolina 27709, USA
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19
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Nondenaturing mass spectrometry to study noncovalent protein/protein and protein/ligand complexes: technical aspects and application to the determination of binding stoichiometries. Methods Mol Biol 2008; 484:217-43. [PMID: 18592183 DOI: 10.1007/978-1-59745-398-1_15] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In the present chapter we detail how mass spectrometry (MS) can be used to characterize noncovalent complexes, especially multimeric proteins and protein/ligand complexes. This original application of MS, also called "supramolecular MS" or "nondenaturing MS," appeared in the early 1990s and has continuously evolved since then. Nondenaturing MS is now fully integrated in structural biology programs and in drug discovery platforms. Indeed, appropriate sample preparation and fine tuning of the instrument make it possible to transfer weak assemblies without disruption from solution into the gas phase of the mass spectrometer. In this chapter we detail experimental conditions (sample preparation, optimization of instrumental parameters, etc.) required for the detection of noncovalent complexes by MS. We then focus on the type of information and accuracy that we get after interpreting electrospray ionization mass spectra obtained under nondenaturing conditions, with emphasis on the determination of the stoichiometry of protein/protein and protein/ligand complexes.
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20
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Benesch JLP, Ruotolo BT, Simmons DA, Robinson CV. Protein complexes in the gas phase: technology for structural genomics and proteomics. Chem Rev 2007; 107:3544-67. [PMID: 17649985 DOI: 10.1021/cr068289b] [Citation(s) in RCA: 344] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Justin L P Benesch
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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21
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Quercia AK, LaMarr WA, Myung J, Ozbal CC, Landro JA, Lumb KJ. High-Throughput Screening by Mass Spectrometry: Comparison with the Scintillation Proximity Assay with a Focused-File Screen of AKT1/PKBα. ACTA ACUST UNITED AC 2007; 12:473-80. [PMID: 17478485 DOI: 10.1177/1087057107300647] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Mass spectrometry is an emerging format for label-free high-throughput screening. The main limitation of mass spectrometry is throughput, due to the requirement to purify samples prior to ionization. Here the authors compare an automated high-throughput mass spectrometry (HTMS) system (RapidFire™) with the scintillation proximity assay (SPA). The cancer therapy target AKT1/PKBα was screened against a focused library of kinase inhibitors and IC50 values determined for all compounds that exhibit > 50% inhibition. A selection of additional compounds that exhibited ≤ 50% inhibition in the primary screen was chosen as controls to confirm inactives. The selection of compounds is expected to identify common actives, common inactives, false positives, and false negatives. Agreement is found between HTMS and SPA in terms of primary hit identification and hit confirmation. ( Journal of Biomolecular Screening 2007:473-480)
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Affiliation(s)
- Andrea K Quercia
- Department of Research Technologies, Bayer Pharmaceuticals Corporation, West Haven, Connecticut 06516, USA
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22
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Shepard W, Haouz A, Graña M, Buschiazzo A, Betton JM, Cole ST, Alzari PM. The crystal structure of Rv0813c from Mycobacterium tuberculosis reveals a new family of fatty acid-binding protein-like proteins in bacteria. J Bacteriol 2006; 189:1899-904. [PMID: 17172346 PMCID: PMC1855704 DOI: 10.1128/jb.01435-06] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene Rv0813c from Mycobacterium tuberculosis, which codes for a hypothetical protein of unknown function, is conserved within the order Actinomycetales but absent elsewhere. The crystal structure of Rv0813c reveals a new family of proteins that resemble the fatty acid-binding proteins (FABPs) found in eukaryotes. Rv0813c adopts the 10-stranded beta-barrel fold typical of FABPs but lacks the double-helix insert that covers the entry to the binding site in the eukaryotic proteins. The barrel encloses a deep cavity, at the bottom of which a small cyclic ligand was found to bind to the hydroxyl group of Tyr192. This residue is part of a conserved Arg-X-Tyr motif much like the triad that binds the carboxylate group of fatty acids in FABPs. Most of the residues forming the internal surface of the cavity are conserved in homologous protein sequences found in CG-rich prokaryotes, strongly suggesting that Rv0813c is a member of a new family of bacterial FABP-like proteins that may have roles in the recognition, transport, and/or storage of small molecules in the bacterial cytosol.
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Affiliation(s)
- William Shepard
- Unité de Biochimie Structurale, CNRS URA 2185, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France
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23
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Hofstadler SA, Sannes-Lowery KA. Applications of ESI-MS in drug discovery: interrogation of noncovalent complexes. Nat Rev Drug Discov 2006; 5:585-95. [PMID: 16816839 DOI: 10.1038/nrd2083] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For many years, analytical mass spectrometry has had numerous supporting roles in the drug development process, including the assessment of compound purity; quantitation of absorption, distribution, metabolism and excretion; and compound-specific pharmacokinetic analyses. More recently, mass spectrometry has emerged as an effective technique for identifying lead compounds on the basis of the characterization of noncovalent ligand-macromolecular target interactions. This approach offers several attractive properties for screening applications in drug discovery compared with other strategies, including the small quantities of target and ligands required, and the capacity to study ligands or targets without having to label them. Here, we review the application of electrospray ionization mass spectrometry to the interrogation of noncovalent complexes, highlighting examples from drug discovery efforts aimed at a range of target classes.
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Affiliation(s)
- Steven A Hofstadler
- Ibis Therapeutics, A Division of ISIS Pharmaceuticals, 1891 Rutherford Road, Carlsbad, California 92008, USA.
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24
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Deng G, Sanyal G. Applications of mass spectrometry in early stages of target based drug discovery. J Pharm Biomed Anal 2006; 40:528-38. [PMID: 16256286 DOI: 10.1016/j.jpba.2005.08.038] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 08/30/2005] [Accepted: 08/30/2005] [Indexed: 10/25/2022]
Abstract
Mass spectrometry (MS) has been applied to drug discovery for many years. With the advent of new ionization techniques, MS has emerged as an important analytical tool in identification and characterization of protein targets, structure elucidation of synthetic compounds, and early drug metabolism and pharmacokinetics studies. Two MS-based strategies, function-based and affinity-based, have been employed in recent years for screening and evaluation of compounds. In the function-based approach, the effects of compounds on the biological activity of a target molecule are measured. In the affinity-based approach, compounds are screened based on their binding affinities to target molecules. The interaction between targets and compounds can be directly evaluated by monitoring the formation of non-covalent target-ligand complexes (direct detection) or indirectly evaluated by detecting the compounds after separating bound compounds from unbound (indirect detection). Various techniques including high performance liquid chromatography (HPLC)-MS, size exclusion chromatography (SEC)-MS, frontal affinity chromatography (FAC)-MS and desorption/ionization on silicon (DIOS)-MS can be applied. The recent advances, relative advantages, and limitations of each MS-based method as a tool in compound screening and compound evaluation in the early stages of drug discovery are discussed in this review.
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Affiliation(s)
- Gejing Deng
- Department of Biochemistry, Infection Drug Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.
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25
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De Vriendt K, Van Driessche G, Devreese B, Bebrone C, Anne C, Frère JM, Galleni M, Van Beeumen J. Monitoring the zinc affinity of the metallo-beta-lactamase CphA by automated nanoESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:180-8. [PMID: 16406807 DOI: 10.1016/j.jasms.2005.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 10/05/2005] [Accepted: 10/14/2005] [Indexed: 05/06/2023]
Abstract
Metallo-beta-lactamases are zinc containing enzymes that are able to hydrolyze and inactivate beta-lactam antibiotics. The subclass B2 enzyme CphA of Aeromonas hydrophila is a unique metallo-beta-lactamase because it degrades only carbapenems efficiently and is only active when it has one zinc ion bound. A zinc titration experiment was used to study the zinc affinity of the wild-type and of several mutant CphA enzymes. It shows that a second Zn(2+) is also bound at high ion concentrations. All samples were analyzed using mass spectrometry in combination with an automated nanoESI source. The metal-free enzyme has a bimodal charge distribution indicative of two conformational states. A completely folded enzyme is detected when the apo-enzyme has bound the first zinc. Intensity ratios of the different enzyme forms were used to deduce the zinc affinities. CphA enzymes mutated in metal ligands show decreased zinc affinity compared to wild-type, especially D120 mutants.
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Affiliation(s)
- Kris De Vriendt
- Laboratory of Protein Biochemistry and Protein Engineering, Ghent University, Ghent, Belgium
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26
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Boernsen KO, Gatzek S, Imbert G. Controlled Protein Precipitation in Combination with Chip-Based Nanospray Infusion Mass Spectrometry. An Approach for Metabolomics Profiling of Plasma. Anal Chem 2005; 77:7255-64. [PMID: 16285673 DOI: 10.1021/ac0508604] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) is a common method for profiling biological samples in metabolomics. However, LC-MS data of metabolomic studies are often affected by high noise levels, retention time shifts, and high variability in signal intensities. With a new chip-based nanoelectrospray source it becomes possible to directly infuse complex biological samples such as plasma without any chromatographic separation beforehand. In combination with highly diluted samples and long data acquisition times, the parallel analysis of hundreds of compounds is now possible. In a proof-of-concept study, 10 human plasma samples from females and males were analyzed with the intention to separate the two groups by their different metabolomes. The reproducibility was so high that statistical analysis of the data could be performed without prior normalization. Two groups of female and male samples were separated by a supervised machine learning algorithm, principal component analysis, and hierarchical clustering. Peaks contributing to the group separation were characterized by accurate mass measurement and MS-MS fragmentation and by spiking experiments. The feasibility of direct sample infusion using the new chip-based nanoelectrospray device opens a new dimension for the rapid parallel analysis of complex biological mixtures.
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Affiliation(s)
- K Olaf Boernsen
- Biomarker Development and Integrative Expression Profiling, Novartis Pharma AG, Basel, Switzerland.
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27
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Benkestock K, Edlund PO, Roeraade J. Electrospray ionization mass spectrometry as a tool for determination of drug binding sites to human serum albumin by noncovalent interaction. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:1637-43. [PMID: 15915474 DOI: 10.1002/rcm.1967] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Most proteins in blood plasma bind ligands. Human serum albumin (HSA) is the main transport protein with a very high capacity for binding of endogenous and exogenous compounds in plasma. Many pharmacokinetic properties of a drug depend on the level of binding to plasma proteins. This work reports studies of noncovalent interactions by means of nanoelectrospray ionization mass spectrometry (nanoESI-MS) for determination of the specific binding of selected drug candidates to HSA. Warfarin, iopanoic acid and digitoxin were chosen as site-specific probes that bind to the main sites of HSA. Two drug candidates and two known binders to HSA were analyzed using a competitive approach. The drugs were incubated with the target protein followed by addition of site-specific probes, one at a time. The drug candidates showed predominant affinity to site I (warfarin site). Naproxen and glyburide showed affinity to both sites I and II. The advantages of nanoESI-MS for these studies are the sensitivity, the absence of labeled molecules and the short method development time.
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Affiliation(s)
- Kurt Benkestock
- Biovitrum AB, Department of Structural Chemistry, SE-112 76, Stockholm, Sweden.
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28
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Zamfir A, Vukelić Z, Bindila L, Peter-Katalinić J, Almeida R, Sterling A, Allen M. Fully-automated chip-based nanoelectrospray tandem mass spectrometry of gangliosides from human cerebellum. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1649-1657. [PMID: 15519233 DOI: 10.1016/j.jasms.2004.08.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2004] [Revised: 08/03/2004] [Accepted: 08/03/2004] [Indexed: 05/24/2023]
Abstract
The introduction of chip-based electrospray (ESI) ion sources into biological mass spectrometry (MS) addressed the fundamental issue of how to analyze minute amounts of complex biological systems. The automation of sample delivery into the MS combined with the chip-based ESI allows for high quality bioanalysis in a high-throughput fashion. These advantages have already been demonstrated in proteomics, direct screening of drugs and drug discovery. As part of our continuing effort to implement automated chip-based mass spectrometry into the field of complex carbohydrate analysis, we hereby report the development of a chipESI MS and MS/MS methodology for the screening of gangliosides. A strategy to characterize a complex ganglioside mixture from human cerebellar tissue, by automated ESIchip-quadrupole time-of-flight (QTOF) MS and MS/MS is presented here. The feasibility of this method, and the general experimental requirements for automated chipESI MS analysis of these carbohydrate species is described.
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Affiliation(s)
- Alina Zamfir
- Institute for Medical Physics and Biophysics, Biomedical Analysis, University of Münster, Münster, Germany.
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29
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Zamfir A, Vakhrushev S, Sterling A, Niebel HJ, Allen M, Peter-Katalinić J. Fully Automated Chip-Based Mass Spectrometry for Complex Carbohydrate System Analysis. Anal Chem 2004; 76:2046-54. [PMID: 15053670 DOI: 10.1021/ac035320q] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbohydrates represent a major class of biopolymers, which occur in nature either as oligosaccharides or glycoconjugates, in which the sugar moiety is linked to proteins or lipids. The significance of mass spectrometry for highly sensitive analysis of complex carbohydrates increased after the introduction of the electrospray ionization and matrix assisted laser desorption/ionization methods and the possibility of tandem MS for sequencing of single molecular species in complex mixtures. Rapid and sensitive characterization of carbohydrates in biological systems by automated nanoscale liquid delivery and chip-based electrospray interface techniques have not been developed so far. In this contribution, the implementation and optimization of a fully automated chip-based nanoelectrospray assembly (NanoMate system), operating in the negative ion mode, in combination with QTOF-tandem MS for mapping/sequencing and computer-assisted structure assignment for carbohydrate components in complex mixtures is presented.
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Affiliation(s)
- Alina Zamfir
- Biomedical Analysis, Institute for Medical Physics and Biophysics, University of Münster, Germany
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30
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De Vriendt K, Sandra K, Desmet T, Nerinckx W, Van Beeumen J, Devreese B. Evaluation of automated nano-electrospray mass spectrometry in the determination of non-covalent protein-ligand complexes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2004; 18:3061-7. [PMID: 15543530 DOI: 10.1002/rcm.1728] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The use of electrospray ionization mass spectrometry (ESI-MS) for studying non-covalent interactions between macromolecules and ligands is well established. ESI-MS can be a useful tool for the determination of dissociation constants between molecules in the gas phase. We validate this method by studying the binding of the catalytic domain of cellobiohydrolase I (CBH I) from Trichoderma reesei to the disaccharide inhibitor cellobiose. The method was further applied to study two newly synthesized cellobiose derivatives (m-iodobenzyl 2-deoxy-2-azido-beta-cellobioside and p-benzyloxybenzyl beta-cellobioside). In a titration experiment, peak areas of different charge states of the free enzyme and the complex were summed in order to determine the dissociation constant. For cellobiose and m-iodobenzyl 2-deoxy-2-azido-beta-cellobioside, the calculated values are in good agreement with those reported from either displacement titration or equilibrium binding experiments in solution. Due to non-specific binding, the dissociation constant of p-benzyloxybenzyl beta-cellobioside does not correspond with the solution-based value. Our results indicate the need for careful interpretation of data sets when using nanoESI to study non-covalent interactions.
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Affiliation(s)
- Kris De Vriendt
- Laboratory of Protein Biochemistry and Protein Engineering, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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31
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:1117-1124. [PMID: 14595863 DOI: 10.1002/jms.413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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32
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Zhang S, Van Pelt CK, Wilson DB. Quantitative determination of noncovalent binding interactions using automated nanoelectrospray mass spectrometry. Anal Chem 2003; 75:3010-8. [PMID: 12964745 DOI: 10.1021/ac034089d] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has proven to be an extremely powerful tool for studying biomolecular structures and noncovalent interactions. Here we report a method using a fully automated, chip-based nanoESI-MS system to determine the dissociation constants (Kd) for the complexes of two different proteins with their ligands. The automated nanoelectrospray system, consisting of the NanoMate and ESI chip, serves functionally as a combination of autosampler and nanoelectrospray ionization source. This system provides all the advantages of conventional nanoelectrospray plus automated, high-throughput analyses without carryover. The automated nanoESI system was used to investigate quantitative noncovalent interactions between ribonuclease A (RNase A) and cytidylic acid ligands (2'-CMP, CTP), a well-characterized model protein-ligand complex, and between an inactive endocellulase mutant (Thermobifida fusca Cel6A D117Acd) and four oligosaccharide ligands (cellotriose, cellotetraose, cellopentaose, cellohexaose). Both titration and competitive binding approaches were performed prior to automated nanoESI-MS analysis with a Q-TOF mass spectrometer. Dissociation constants for each complex were calculated from the sum of ion peak areas of free and complexed proteins during the titration and competition experiments. The measured Kd values for the RNase A-CMP and Cel6A D117Acd-G3 complexes were found to be in excellent agreement with the available published values obtained by standard spectroscopic titration techniques. To our knowledge, this is the first report of using an ESI-MS approach to study the interactions between a cellulase and oligosaccharides. The results provide new insights for understanding the nature of cellulase-cellulose interactions.
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Affiliation(s)
- Sheng Zhang
- Advion BioSciences, Inc., 15 Catherwood Road, Ithaca, New York 14850, USA.
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