1
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Li J, Morato NM, Westover LS, Abeywickrema P, Geng J, Piassek M, Harden D, Strambeanu I, Shi Z, Cooks RG, Meng J. High-Throughput Assessment of Bile Salt Export Pump Inhibition Using RapidFire-MS and DESI-MS. ACS Med Chem Lett 2024; 15:1584-1590. [PMID: 39291028 PMCID: PMC11403724 DOI: 10.1021/acsmedchemlett.4c00302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/01/2024] [Accepted: 08/08/2024] [Indexed: 09/19/2024] Open
Abstract
The bile salt export pump (BSEP) assay is widely used to evaluate the potential for drug-induced liver injury (DILI) early in the drug discovery process. While traditional liquid chromatography-mass spectrometry (LC-MS)-based approaches have been utilized for BSEP activity testing, they have intrinsic limitations in either throughput or the requirement for sample preparation and are difficult to scale up in order to screen drug candidates. Here we demonstrate the use of two different high-throughput MS methods based on solid-phase extraction (SPE) and desorption electrospray ionization (DESI) for high-throughput BSEP activity assessment in a label-free manner, with minimal needs for sample workup, at sampling rates of ∼11 and ∼5.5 s/sample, respectively. Both approaches were validated, compared, and successfully applied to the evaluation of 96 drug candidates for the inhibition of taurocholic acid (TCA) transport using BSEP vesicles.
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Affiliation(s)
- Jie Li
- Global Discovery Chemistry, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nicolás M Morato
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lori S Westover
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Pravien Abeywickrema
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Jieping Geng
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Madison Piassek
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - David Harden
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Iulia Strambeanu
- Global Discovery Chemistry, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Zhicai Shi
- Global Discovery Chemistry, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Juncai Meng
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
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2
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Pinto MF, Sirina J, Holliday ND, McWhirter CL. High-throughput kinetics in drug discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100170. [PMID: 38964171 DOI: 10.1016/j.slasd.2024.100170] [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: 04/05/2024] [Revised: 05/21/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
Abstract
The importance of a drug's kinetic profile and interplay of structure-kinetic activity with PK/PD has long been appreciated in drug discovery. However, technical challenges have often limited detailed kinetic characterization of compounds to the latter stages of projects. This review highlights the advances that have been made in recent years in techniques, instrumentation, and data analysis to increase the throughput of detailed kinetic and mechanistic characterization, enabling its application earlier in the drug discovery process.
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Affiliation(s)
- Maria Filipa Pinto
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom
| | - Julija Sirina
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom
| | - Nicholas D Holliday
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom; School of Life Sciences, The Medical School, University of Nottingham, Nottingham, NG7 2UH, United Kingdom
| | - Claire L McWhirter
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom.
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3
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Reder GK, Bjurström EY, Brunnsåker D, Kronström F, Lasin P, Tiukova I, Savolainen OI, Dodds JN, May JC, Wikswo JP, McLean JA, King RD. AutonoMS: Automated Ion Mobility Metabolomic Fingerprinting. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:542-550. [PMID: 38310603 PMCID: PMC10921458 DOI: 10.1021/jasms.3c00396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 02/06/2024]
Abstract
Automation is dramatically changing the nature of laboratory life science. Robotic lab hardware that can perform manual operations with greater speed, endurance, and reproducibility opens an avenue for faster scientific discovery with less time spent on laborious repetitive tasks. A major bottleneck remains in integrating cutting-edge laboratory equipment into automated workflows, notably specialized analytical equipment, which is designed for human usage. Here we present AutonoMS, a platform for automatically running, processing, and analyzing high-throughput mass spectrometry experiments. AutonoMS is currently written around an ion mobility mass spectrometry (IM-MS) platform and can be adapted to additional analytical instruments and data processing flows. AutonoMS enables automated software agent-controlled end-to-end measurement and analysis runs from experimental specification files that can be produced by human users or upstream software processes. We demonstrate the use and abilities of AutonoMS in a high-throughput flow-injection ion mobility configuration with 5 s sample analysis time, processing robotically prepared chemical standards and cultured yeast samples in targeted and untargeted metabolomics applications. The platform exhibited consistency, reliability, and ease of use while eliminating the need for human intervention in the process of sample injection, data processing, and analysis. The platform paves the way toward a more fully automated mass spectrometry analysis and ultimately closed-loop laboratory workflows involving automated experimentation and analysis coupled to AI-driven experimentation utilizing cutting-edge analytical instrumentation. AutonoMS documentation is available at https://autonoms.readthedocs.io.
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Affiliation(s)
- Gabriel K. Reder
- Department
of Computer Science and Engineering, Chalmers
University of Technology, Gothenburg 412 96, Sweden
- Department
of Applied Physics, SciLifeLab, KTH Royal
Institute of Technology, Solna 171 21, Sweden
| | - Erik Y. Bjurström
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg 412 96, Sweden
| | - Daniel Brunnsåker
- Department
of Computer Science and Engineering, Chalmers
University of Technology, Gothenburg 412 96, Sweden
| | - Filip Kronström
- Department
of Computer Science and Engineering, Chalmers
University of Technology, Gothenburg 412 96, Sweden
| | - Praphapan Lasin
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg 412 96, Sweden
| | - Ievgeniia Tiukova
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg 412 96, Sweden
| | - Otto I. Savolainen
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg 412 96, Sweden
- Institute
of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio 702 11, Finland
| | - James N. Dodds
- Chemistry
Department, The University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jody C. May
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John P. Wikswo
- Vanderbilt
Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - John A. McLean
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ross D. King
- Department
of Computer Science and Engineering, Chalmers
University of Technology, Gothenburg 412 96, Sweden
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, U.K.
- The Alan
Turing Institute, London NW1 2DB, U.K.
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4
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Williams JD, Pu F, Sawicki JW, Elsen NL. Ultra-high-throughput mass spectrometry in drug discovery: fundamentals and recent advances. Expert Opin Drug Discov 2024; 19:291-301. [PMID: 38111363 DOI: 10.1080/17460441.2023.2293153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
INTRODUCTION Ultra-high-throughput mass spectrometry, uHT-MS, is a technology that utilizes ionization and sample delivery technologies optimized to enable sampling from well plates at > 1 sample per second. These technologies do not need a chromatographic separation step and can be utilized in a wide variety of assays to detect a broad range of analytes including small molecules, lipids, and proteins. AREAS COVERED This manuscript provides a brief historical review of high-throughput mass spectrometry and the recently developed technologies that have enabled uHT-MS. The report also provides examples and references on how uHT-MS has been used in biochemical and chemical assays, nuisance compound profiling, protein analysis and high throughput experimentation for chemical synthesis. EXPERT OPINION The fast analysis time provided by uHT-MS is transforming how biochemical and chemical assays are performed in drug discovery. The potential to associate phenotypic responses produced by 1000's of compound treatments with changes in endogenous metabolite and lipid signals is becoming feasible. With the augmentation of simple, fast, high-throughput sample preparation, the scope of uHT-MS usage will increase. However, it likely will not supplant LC-MS for analyses that require low detection limits from complex matrices or characterization of complex biotherapeutics such as antibody-drug conjugates.
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Affiliation(s)
| | - Fan Pu
- Abbvie Discovery Research, North Chicago, IL, USA
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5
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Papp LA, Imre S, Bálint I, Lungu AI, Mărcutiu PE, Papp J, Ion V. Is it Time to Migrate to Liquid Chromatography Automated Platforms in the Clinical Laboratory? A Brief Point of View. J Chromatogr Sci 2024; 62:191-200. [PMID: 36715315 DOI: 10.1093/chromsci/bmad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/28/2022] [Indexed: 01/31/2023]
Abstract
Liquid chromatography coupled to mass spectrometry already started to surpass the major drawbacks in terms of sensitivity, specificity and cross-reactivity that some analytical methods used in the clinical laboratory exhibit. This hyphenated technique is already preferred for specific applications while finding its own place in the clinical laboratory setting. However, large-scale usage, high-throughput analysis and lack of automation emerge as shortcomings that liquid chromatography coupled to mass spectrometry still has to overrun in order to be used on a larger scale in the clinical laboratory. The aim of this review article is to point out the present-day position of the liquid chromatography coupled to mass spectrometry technique while trying to understand how this analytical method relates to the basic working framework of the clinical laboratory. This paper offers insights about the main regulation and traceability criteria that this coupling method has to align and comply to, automation and standardization issues and finally the critical steps in sample preparation workflows all related to the high-throughput analysis framework. Further steps are to be made toward automation, speed and easy-to-use concept; however, the current technological and quality premises are favorable for chromatographic coupled to mass spectral methods.
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Affiliation(s)
- Lajos-Attila Papp
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Public Health Department Mures, Gheorghe Marinescu street 40, 540136 Targu Mures, Romania
| | - Silvia Imre
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
| | - István Bálint
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Public Health Department Mures, Gheorghe Marinescu street 40, 540136 Targu Mures, Romania
| | - Andreea-Ioana Lungu
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Public Health Department Mures, Gheorghe Marinescu street 40, 540136 Targu Mures, Romania
| | - Petra-Edina Mărcutiu
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Public Health Department Mures, Gheorghe Marinescu street 40, 540136 Targu Mures, Romania
| | - Júlia Papp
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Public Health Department Mures, Gheorghe Marinescu street 40, 540136 Targu Mures, Romania
| | - Valentin Ion
- Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
- Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science, and Technology from Targu Mures, Gheorghe Marinescu street 38, 540142 Targu Mures, Romania
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6
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Juliano BR, Keating JW, Li HW, Anders AG, Xie Z, Ruotolo BT. Development of an Automated, High-Throughput Methodology for Native Mass Spectrometry and Collision-Induced Unfolding. Anal Chem 2023; 95:16717-16724. [PMID: 37924308 PMCID: PMC11081713 DOI: 10.1021/acs.analchem.3c03788] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Native ion mobility mass spectrometry (nIM-MS) has emerged as a useful technology for the rapid evaluation of biomolecular structures. When combined with collisional activation in a collision-induced unfolding (CIU) experiment, nIM-MS experimentation can be leveraged to gain greater insight into biomolecular conformation and stability. However, nIM-MS and CIU remain throughput limited due to nonautomated sample preparation and introduction. Here, we explore the use of a RapidFire robotic sample handling system to develop an automated, high-throughput methodology for nMS and CIU. We describe native RapidFire-MS (nRapidFire-MS) capable of performing online desalting and sample introduction in as little as 10 s per sample. When combined with CIU, our nRapidFire-MS approach can be used to collect CIU fingerprints in 30 s following desalting by using size exclusion chromatography cartridges. When compared to nMS and CIU data collected using standard approaches, ion signals recorded by nRapidFire-MS exhibit identical ion collision cross sections, indicating that the same conformational populations are tracked by the two approaches. Our data further suggest that nRapidFire-MS can be extended to study a variety of biomolecular classes, including proteins and protein complexes ranging from 5 to 300 kDa and oligonucleotides. Furthermore, nRapidFire-MS data acquired for biotherapeutics suggest that nRapidFire-MS has the potential to enable high-throughput nMS analyses of biopharmaceutical samples. We conclude by discussing the potential of nRapidFire-MS for enabling the development of future CIU assays capable of catalyzing breakthroughs in protein engineering, inhibitor discovery, and formulation development for biotherapeutics.
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Affiliation(s)
- Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph W Keating
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Henry W Li
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anna G Anders
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zhuoer Xie
- Attribute Sciences, Process Development, Amgen, Thousand Oaks, California 91320, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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7
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Talaty NN, Johnson RW, Sawicki J, Nacham O, Djuric SW. Recent Developments in Mass Spectrometry to Support Next-Generation Synthesis and Screening. ACS Med Chem Lett 2023; 14:711-718. [PMID: 37312853 PMCID: PMC10258828 DOI: 10.1021/acsmedchemlett.3c00040] [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: 02/02/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
The complexity of new therapeutics continues to increase and the timeline for the discovery of these therapeutics continues to shrink. This creates demand for new analytical techniques to facilitate quicker discovery and development of novel drugs. Mass spectrometry is one of the most prolific analytical techniques that has been applied across the entire drug discovery pipeline. New mass spectrometers and the associated methods for sampling have been introduced at a rate that keeps pace with new chemistries, therapeutic types, and screening practices used by modern drug hunters. This microperspective covers application and implementation of new mass spectrometry workflows that enable current and future efforts in screening and synthesis for drug discovery.
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Affiliation(s)
- Nari N. Talaty
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Robert W. Johnson
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - James Sawicki
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Omprakash Nacham
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Stevan W. Djuric
- Discovery
Chemistry and Technology Consulting LLC, New Bern, North Carolina 28562, United States
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8
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Pu F, Radosevich AJ, Bruckner BG, Fontaine DA, Panchal SC, Williams JD, Gopalakrishnan SM, Elsen NL. New Platform for Label-Free, Proximal Cellular Pharmacodynamic Assays: Identification of Glutaminase Inhibitors Using Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry. ACS Chem Biol 2023; 18:942-948. [PMID: 37043689 DOI: 10.1021/acschembio.3c00087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Cellular pharmacodynamic assays are crucial aspects of lead optimization programs in drug discovery. These assays are sometimes difficult to develop, oftentimes distal from the target and frequently low throughput, which necessitates their incorporation in the drug discovery funnel later than desired. The earlier direct pharmacodynamic modulation of a target can be established, the fewer resources are wasted on compounds that are acting via an off-target mechanism. Mass spectrometry is a versatile tool that is often used for direct, proximal cellular pharmacodynamic assay analysis, but liquid chromatography-mass spectrometry methods are low throughput and are unable to fully support structure-activity relationship efforts in early medicinal chemistry programs. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is an ambient ionization method amenable to high-throughput cellular assays, capable of diverse analyte detection, ambient and rapid laser sampling processes, and low cross-contamination. Here, we demonstrate the capability of IR-MALDESI for the detection of diverse analytes directly from cells and report the development of a high-throughput, label-free, proximal cellular pharmacodynamic assay using IR-MALDESI for the discovery of glutaminase inhibitors and a biochemical assay for hit confirmation. We demonstrate the throughput with a ∼100,000-compound cellular screen. Hits from the screening were confirmed by retesting in dose-response with mass spectrometry-based cellular and biochemical assays. A similar workflow can be applied to other targets with minimal modifications, which will speed up the discovery of cell active lead series and minimize wasted chemistry resources on off-target mechanisms.
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Affiliation(s)
- Fan Pu
- Discovery Research, AbbVie Inc., 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Andrew J Radosevich
- Discovery Research, AbbVie Inc., 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Brett G Bruckner
- Discovery Research, AbbVie Inc., 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - David A Fontaine
- Discovery Research, AbbVie Inc., 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Sanjay C Panchal
- Discovery Research, AbbVie Inc., 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Jon D Williams
- Discovery Research, AbbVie Inc., 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Sujatha M Gopalakrishnan
- Discovery Research, AbbVie Inc., 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Nathaniel L Elsen
- Discovery Research, AbbVie Inc., 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
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9
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Sellés Vidal L, Isalan M, Heap JT, Ledesma-Amaro R. A primer to directed evolution: current methodologies and future directions. RSC Chem Biol 2023; 4:271-291. [PMID: 37034405 PMCID: PMC10074555 DOI: 10.1039/d2cb00231k] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
Directed evolution is one of the most powerful tools for protein engineering and functions by harnessing natural evolution, but on a shorter timescale. It enables the rapid selection of variants of biomolecules with properties that make them more suitable for specific applications. Since the first in vitro evolution experiments performed by Sol Spiegelman in 1967, a wide range of techniques have been developed to tackle the main two steps of directed evolution: genetic diversification (library generation), and isolation of the variants of interest. This review covers the main modern methodologies, discussing the advantages and drawbacks of each, and hence the considerations for designing directed evolution experiments. Furthermore, the most recent developments are discussed, showing how advances in the handling of ever larger library sizes are enabling new research questions to be tackled.
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Affiliation(s)
- Lara Sellés Vidal
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
| | - Mark Isalan
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
- School of Life Sciences, The University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
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10
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Dueñas ME, Peltier‐Heap RE, Leveridge M, Annan RS, Büttner FH, Trost M. Advances in high-throughput mass spectrometry in drug discovery. EMBO Mol Med 2023; 15:e14850. [PMID: 36515561 PMCID: PMC9832828 DOI: 10.15252/emmm.202114850] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 12/15/2022] Open
Abstract
High-throughput (HT) screening drug discovery, during which thousands or millions of compounds are screened, remains the key methodology for identifying active chemical matter in early drug discovery pipelines. Recent technological developments in mass spectrometry (MS) and automation have revolutionized the application of MS for use in HT screens. These methods allow the targeting of unlabelled biomolecules in HT assays, thereby expanding the breadth of targets for which HT assays can be developed compared to traditional approaches. Moreover, these label-free MS assays are often cheaper, faster, and more physiologically relevant than competing assay technologies. In this review, we will describe current MS techniques used in drug discovery and explain their advantages and disadvantages. We will highlight the power of mass spectrometry in label-free in vitro assays, and its application for setting up multiplexed cellular phenotypic assays, providing an exciting new tool for screening compounds in cell lines, and even primary cells. Finally, we will give an outlook on how technological advances will increase the future use and the capabilities of mass spectrometry in drug discovery.
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Affiliation(s)
- Maria Emilia Dueñas
- Laboratory for Biomedical Mass Spectrometry, Biosciences InstituteNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Rachel E Peltier‐Heap
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Melanie Leveridge
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Roland S Annan
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Frank H Büttner
- Drug Discovery Sciences, High Throughput BiologyBoehringer Ingelheim Pharma GmbH&CoKGBiberachGermany
| | - Matthias Trost
- Laboratory for Biomedical Mass Spectrometry, Biosciences InstituteNewcastle UniversityNewcastle‐upon‐TyneUK
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11
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Müller L, Burton AK, Tayler CL, Rowedder JE, Hutchinson JP, Peace S, Quayle JM, Leveridge MV, Annan RS, Trost M, Peltier-Heap RE, Dueñas ME. A high-throughput MALDI-TOF MS biochemical screen for small molecule inhibitors of the antigen aminopeptidase ERAP1. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:3-11. [PMID: 36414185 DOI: 10.1016/j.slasd.2022.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
MALDI-TOF MS is a powerful analytical technique that provides a fast and label-free readout for in vitro assays in the high-throughput screening (HTS) environment. Here, we describe the development of a novel, HTS compatible, MALDI-TOF MS-based drug discovery assay for the endoplasmic reticulum aminopeptidase 1 (ERAP1), an important target in immuno-oncology and auto-immune diseases. A MALDI-TOF MS assay was developed beginning with an already established ERAP1 RapidFire MS (RF MS) assay, where the peptide YTAFTIPSI is trimmed into the product TAFTIPSI. We noted low ionisation efficiency of these peptides in MALDI-TOF MS and hence incorporated arginine residues into the peptide sequences to improve ionisation. The optimal assay conditions were established with these new basic assay peptides on the MALDI-TOF MS platform and validated with known ERAP1 inhibitors. Assay stability, reproducibility and robustness was demonstrated on the MALDI-TOF MS platform. From a set of 699 confirmed ERAP1 binders, identified in a prior affinity selection mass spectrometry (ASMS) screen, active compounds were determined at single concentration and in a dose-response format with the new MALDI-TOF MS setup. Furthermore, to allow for platform performance comparison, the same compound set was tested on the established RF MS setup, as the new basic peptides showed fragmentation in ESI-MS. The two platforms showed a comparable performance, but the MALDI-TOF MS platform had several advantages, such as shorter sample cycle times, reduced reagent consumption, and a lower tight-binding limit.
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Affiliation(s)
- Leonie Müller
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom
| | - Amy K Burton
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Chloe L Tayler
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - James E Rowedder
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Jonathan P Hutchinson
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Simon Peace
- GSK, Medicinal Chemistry, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Julie M Quayle
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Melanie V Leveridge
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Roland S Annan
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Matthias Trost
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom.
| | | | - Maria Emilia Dueñas
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom.
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12
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Khan SA, Nidhi FNU, Amendum PC, Tomatsu S. Detection of Glycosaminoglycans in Biological Specimens. Methods Mol Biol 2023; 2619:3-24. [PMID: 36662458 PMCID: PMC10199356 DOI: 10.1007/978-1-0716-2946-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Proteoglycans (PGs) are macromolecules formed by a protein backbone to which one or more glycosaminoglycan (GAG) side chains are covalently attached. Most PGs are present in connective tissues, cell surfaces, and intracellular compartments. The major biological function of PGs derives from the GAG component of the molecule, which is involved in cell growth and proliferation, embryogenesis, maintenance of tissue hydration, and interactions of the cells via receptors. PGs are categorized into four groups based on their cellular and subcellular localization, including cell surfaces and extracellular, intracellular, and pericellular locations. GAGs are a crucial component of PGs involved in various physiological and pathological processes. GAGs also serve as biomarkers of metabolic diseases such as mucopolysaccharidoses and mucolipidoses. Detection of specific GAGs in various biological fluids helps manage various genetic metabolic disorders before it causes irreversible damage to the patient (Amendum et al., Diagnostics (Basel) 11(9):1563, 2021). There are several methods for detecting GAGs; this chapter focuses on measuring GAGs using enzyme-linked immunosorbent assay, liquid chromatographic tandem mass spectrometry, and automated high-throughput mass spectrometry.
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Affiliation(s)
- Shaukat A Khan
- Department of Biomedical Research, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE, USA
| | - F N U Nidhi
- Department of Biomedical Research, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE, USA
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Paige C Amendum
- Department of Biomedical Research, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE, USA
| | - Shunji Tomatsu
- Department of Biomedical Research, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE, USA.
- Department of Pediatrics, Shimane University, Izumo, Japan.
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan.
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA.
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13
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Luo YS, Chen Z, Hsieh NH, Lin TE. Chemical and biological assessments of environmental mixtures: A review of current trends, advances, and future perspectives. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128658. [PMID: 35290896 DOI: 10.1016/j.jhazmat.2022.128658] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/21/2022] [Accepted: 03/07/2022] [Indexed: 05/28/2023]
Abstract
Considering the chemical complexity and toxicity data gaps of environmental mixtures, most studies evaluate the chemical risk individually. However, humans are usually exposed to a cocktail of chemicals in real life. Mixture health assessment remains to be a research area having significant knowledge gaps. Characterization of chemical composition and bioactivity/toxicity are the two critical aspects of mixture health assessments. This review seeks to introduce the recent progress and tools for the chemical and biological characterization of environmental mixtures. The state-of-the-art techniques include the sampling, extraction, rapid detection methods, and the in vitro, in vivo, and in silico approaches to generate the toxicity data of an environmental mixture. Application of these novel methods, or new approach methodologies (NAMs), has increased the throughput of generating chemical and toxicity data for mixtures and thus refined the mixture health assessment. Combined with computational methods, the chemical and biological information would shed light on identifying the bioactive/toxic components in an environmental mixture.
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Affiliation(s)
- Yu-Syuan Luo
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, Taipei City, Taiwan.
| | - Zunwei Chen
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nan-Hung Hsieh
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Tzu-En Lin
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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14
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Knizner KT, Bagley MC, Pu F, Elsen NL, Williams JD, Muddiman DC. Normalization techniques for high-throughput screening by infrared matrix-assisted laser desorption electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4869. [PMID: 35678360 PMCID: PMC9287052 DOI: 10.1002/jms.4869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/21/2022] [Accepted: 05/26/2022] [Indexed: 05/29/2023]
Abstract
Mass spectrometry (MS) is an effective analytical tool for high-throughput screening (HTS) in the drug discovery field. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) MS is a high-throughput platform that has achieved analysis times of sub-seconds-per-sample. Due to the high-throughput analysis speed, methods are needed to increase the analyte signal while decreasing the variability in IR-MALDESI-MS analyses to improve data quality and reduce false-positive hits. The Z-factor is used as a statistic of assay quality that can be improved by reducing the variation of target ion abundances or increasing signal. Herein we report optimal solvent compositions for increasing measured analyte abundances with direct analysis by IR-MALDESI-MS. We also evaluate normalization strategies, such as adding a normalization standard that is similar or dissimilar in structure to the model target drug, to reduce the variability of measured analyte abundances with direct analyses by IR-MALDESI-MS in both positive and negative ionization modes.
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Affiliation(s)
- Kevan T. Knizner
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Michael C. Bagley
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Fan Pu
- Drug Discovery Science and TechnologyAbbVie Inc.North ChicagoIllinoisUSA
| | - Nathaniel L. Elsen
- Drug Discovery Science and TechnologyAbbVie Inc.North ChicagoIllinoisUSA
| | - Jon D. Williams
- Drug Discovery Science and TechnologyAbbVie Inc.North ChicagoIllinoisUSA
| | - David C. Muddiman
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Molecular Education, Technology and Research Innovation Center (METRIC)North Carolina State UniversityRaleighNorth CarolinaUSA
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15
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Liu C. Acoustic Ejection Mass Spectrometry: Fundamentals and Applications in High-Throughput Drug Discovery. Expert Opin Drug Discov 2022; 17:775-787. [DOI: 10.1080/17460441.2022.2084069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Chang Liu
- SCIEX, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada
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16
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Towards one sample per second for mass spectrometric screening of engineered microbial strains. Curr Opin Biotechnol 2022; 76:102725. [PMID: 35489307 DOI: 10.1016/j.copbio.2022.102725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 03/03/2022] [Accepted: 03/20/2022] [Indexed: 12/11/2022]
Abstract
Microbial cell factories convert renewable feedstocks into desirable chemicals and materials. Due to the lack of predictive modeling, high-throughput screening remains essential for microbial strain engineering. Mass spectrometry (MS) is a label-free modality with superior sensitivity and chemical specificity. Critical advances in improving the throughput of MS assays on complex microbial samples include massively parallel cultivation, robotic sample preparation, and chromatography-free instrumentation. Here, we review the recent development and application of rapid MS assays in screening microbial libraries, achieving or approaching a rate of one sample per second. We conclude with unique challenges associated with MS screening of strain libraries and discuss future solutions.
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17
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Krenkel H, Brown J, Richardson K, Hoyes E, Morris M, Cramer R. Ultrahigh-Throughput Sample Analysis Using Liquid Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Anal Chem 2022; 94:4141-4145. [PMID: 35234449 PMCID: PMC9385107 DOI: 10.1021/acs.analchem.1c05614] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Mass
spectrometry (MS) allows for automated analysis of complex
samples at high resolution without the need for labeling/derivatization.
Liquid atmospheric pressure matrix-assisted laser desorption/ionization
(LAP-MALDI) enables rapid sample preparation and MS analysis using
microtiter-plate formats and high-performing mass spectrometers. We
present a step change in high-speed, large-scale MS sample analysis
of peptides at 20 samples/s and an enzymatic assay at 40 samples/s,
i.e., an order of magnitude faster than current MS platforms. LAP-MALDI
requires only low amounts of sample volume (<2 μL), of which
only a fraction (<1%) is typically consumed, and allows for multiplexing
and high-speed MS/MS analysis, demonstrated at ∼10 samples/s.
Its high ion signal stability and similarity to electrospray ionization
enables CVs below 10% and the analysis of multiply charged peptide
ions at these extreme speeds. LAP-MALDI MS fulfills the speed requirements
for large-scale population diagnostics and compound screening with
the potential of analyzing >1 million samples per day.
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Affiliation(s)
- Henriette Krenkel
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, U.K
| | - Jeffery Brown
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | | | - Emmy Hoyes
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | - Michael Morris
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, U.K
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18
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Knizner KT, Bagley MC, Garrard KP, Hauschild JP, Pu F, Elsen NL, Williams JD, Muddiman DC. Optimized C-Trap Timing of an Orbitrap 240 Mass Spectrometer for High-Throughput Screening and Native MS by IR-MALDESI. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:328-334. [PMID: 35073091 PMCID: PMC9944060 DOI: 10.1021/jasms.1c00319] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Infrared matrix-assisted laser desorption ionization (IR-MALDESI) is a hybrid mass spectrometry ionization source that combines the benefits of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) making it a great analytical tool for high-throughput screening (HTS) analyses. IR-MALDESI is coupled to an Orbitrap Exploris 240 mass spectrometer that utilizes a bent quadrupole (C-trap) to inject accumulated ions into the high-field Orbitrap mass analyzer. Here, we present a study on the optimized C-trap timing for HTS analyses by IR-MALDESI mass spectrometry. The timing between initial ion generation and the C-trap opening time was optimized to reduce unnecessary ambient ion accumulation in the mass spectrometer. The time in which the C-trap was held open, the ion accumulation time, was further optimized to maximize the accumulation of analyte ions generated using IR-MALDESI. The resulting C-trap opening scheme benefits small-molecule HTS analyses by IR-MALDESI by maximizing target ion abundances, minimizing ambient ion abundances, and minimizing the total analysis time per sample. The proposed C-trap timing scheme for HTS does not translate to large molecules; a NIST monoclonal antibody standard reference material was analyzed to demonstrate that larger analytes require longer ion accumulation times and that IR-MALDESI can measure intact antibodies in their native state.
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Affiliation(s)
- Kevan T. Knizner
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Michael C. Bagley
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Kenneth P. Garrard
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
- Precision Engineering Consortium, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Fan Pu
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, USA
| | - Nathaniel L. Elsen
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, USA
| | - Jon D. Williams
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, USA
| | - David C. Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
- Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC 27695, USA
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19
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Satapati S, Downes DP, Metzger D, Shankaran H, Talukdar S, Zhou Y, Ren Z, Chen M, Lim YH, Hatcher NG, Wen X, Sheth PR, McLaren DG, Previs SF. Using measures of metabolic flux to align screening and clinical development: Avoiding pitfalls to enable translational studies. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:20-28. [PMID: 35058172 DOI: 10.1016/j.slasd.2021.10.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Screening campaigns, especially those aimed at modulating enzyme activity, often rely on measuring substrate→product conversions. Unfortunately, the presence of endogenous substrates and/or products can limit one's ability to measure conversions. As well, coupled detection systems, often used to facilitate optical readouts, are subject to interference. Stable isotope labeled substrates can overcome background contamination and yield a direct readout of enzyme activity. Not only can isotope kinetic assays enable early screening, but they can also be used to follow hit progression in translational (pre)clinical studies. Herein, we consider a case study surrounding lipid biology to exemplify how metabolic flux analyses can connect stages of drug development, caveats are highlighted to ensure reliable data interpretations. For example, when measuring enzyme activity in early biochemical screening it may be enough to quantify the formation of a labeled product. In contrast, cell-based and in vivo studies must account for variable exposure to a labeled substrate (or precursor) which occurs via tracer dilution and/or isotopic exchange. Strategies are discussed to correct for these complications. We believe that measures of metabolic flux can help connect structure-activity relationships with pharmacodynamic mechanisms of action and determine whether mechanistically differentiated biophysical interactions lead to physiologically relevant outcomes. Adoption of this logic may allow research programs to (i) build a critical bridge between primary screening and (pre)clinical development, (ii) elucidate biology in parallel with screening and (iii) suggest a strategy aimed at in vivo biomarker development.
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Affiliation(s)
- Santhosh Satapati
- Merck & Co., Inc, 213 E. Grand Ave, South San Francisco, CA, 94080, USA
| | - Daniel P Downes
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Daniel Metzger
- Merck & Co., Inc, 213 E. Grand Ave, South San Francisco, CA, 94080, USA
| | - Harish Shankaran
- Merck & Co., Inc, 213 E. Grand Ave, South San Francisco, CA, 94080, USA
| | - Saswata Talukdar
- Merck & Co., Inc, 213 E. Grand Ave, South San Francisco, CA, 94080, USA
| | - Yingjiang Zhou
- Merck & Co., Inc, 213 E. Grand Ave, South San Francisco, CA, 94080, USA
| | - Zhao Ren
- Merck & Co., Inc, 213 E. Grand Ave, South San Francisco, CA, 94080, USA
| | - Michelle Chen
- Merck & Co., Inc, 213 E. Grand Ave, South San Francisco, CA, 94080, USA
| | - Yeon-Hee Lim
- Merck & Co., Inc, 213 E. Grand Ave, South San Francisco, CA, 94080, USA
| | - Nathan G Hatcher
- Merck & Co., Inc, 770 Sumneytown Pike, West Point, PA, 19486, USA
| | - Xiujuan Wen
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Payal R Sheth
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - David G McLaren
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Stephen F Previs
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA.
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20
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Scholle MD, McLaughlin D, Gurard-Levin ZA. High-Throughput Affinity Selection Mass Spectrometry Using SAMDI-MS to Identify Small-Molecule Binders of the Human Rhinovirus 3C Protease. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:974-983. [PMID: 34151629 DOI: 10.1177/24725552211023211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Affinity selection mass spectrometry (ASMS) has emerged as a powerful high-throughput screening tool used in drug discovery to identify novel ligands against therapeutic targets. This report describes the first high-throughput screen using a novel self-assembled monolayer desorption ionization (SAMDI)-ASMS methodology to reveal ligands for the human rhinovirus 3C (HRV3C) protease. The approach combines self-assembled monolayers of alkanethiolates on gold with matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry (MS), a technique termed SAMDI-ASMS. The primary screen of more than 100,000 compounds in pools of 8 compounds per well was completed in less than 8 h, and informs on the binding potential and selectivity of each compound. Initial hits were confirmed in follow-up SAMDI-ASMS experiments in single-concentration and dose-response curves. The ligands identified by SAMDI-ASMS were further validated using differential scanning fluorimetry (DSF) and in functional protease assays against HRV3C and the related SARS-CoV-2 3CLpro enzyme. SAMDI-ASMS offers key benefits for drug discovery over traditional ASMS approaches, including the high-throughput workflow and readout, minimizing compound misbehavior by using smaller compound pools, and up to a 50-fold reduction in reagent consumption. The flexibility of this novel technology opens avenues for high-throughput ASMS assays of any target, thereby accelerating drug discovery for diverse diseases.
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21
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Simon RP, Häbe TT, Ries R, Winter M, Wang Y, Fernández-Montalván A, Bischoff D, Runge F, Reindl W, Luippold AH, Büttner FH. Acoustic Ejection Mass Spectrometry: A Fully Automatable Technology for High-Throughput Screening in Drug Discovery. SLAS DISCOVERY 2021; 26:961-973. [PMID: 34308708 DOI: 10.1177/24725552211028135] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Acoustic droplet ejection (ADE)-open port interface (OPI)-mass spectrometry (MS) has recently been introduced as a versatile analytical method that combines fast and contactless acoustic sampling with sensitive and accurate electrospray ionization (ESI)-MS-based analyte detection. The potential of the technology to provide label-free measurements in subsecond analytical cycle times makes it an attractive option for high-throughput screening (HTS). Here, we report the first implementation of ADE-OPI-MS in a fully automated HTS environment, based on the example of a biochemical assay aiming at the identification of small-molecule inhibitors of the cyclic guanosine monophosphate-adenosine monophosphate (GMP-AMP) synthase (cGAS). First, we describe the optimization of the method to enable sensitive and accurate determination of enzyme activity and inhibition in miniaturized 1536-well microtiter plate format. Then we show both results from a validation single-concentration screen using a test set of 5500 compounds, and the subsequent concentration-response testing of selected hits in direct comparison with a previously established matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) readout. Finally, we present the development of an in-line OPI cleaning procedure aiming to match the instrument robustness required for large-scale HTS campaigns. Overall, this work points to critical method development parameters and provides guidance for the establishment of integrated ADE-OPI-MS as HTS-compatible technology for early drug discovery.
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Affiliation(s)
- Roman P Simon
- Drug Discovery Sciences, Boehringer Ingelheim Pharma, Biberach an der Riß, Germany
| | - Tim T Häbe
- Drug Discovery Sciences, Boehringer Ingelheim Pharma, Biberach an der Riß, Germany
| | - Robert Ries
- Drug Discovery Sciences, Boehringer Ingelheim Pharma, Biberach an der Riß, Germany
| | - Martin Winter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma, Biberach an der Riß, Germany
| | - Yuting Wang
- Drug Discovery Sciences, Boehringer Ingelheim Pharma, Biberach an der Riß, Germany
| | | | - Daniel Bischoff
- Drug Discovery Sciences, Boehringer Ingelheim Pharma, Biberach an der Riß, Germany
| | - Frank Runge
- Drug Discovery Sciences, Boehringer Ingelheim Pharma, Biberach an der Riß, Germany
| | - Wolfgang Reindl
- Drug Discovery Sciences, Boehringer Ingelheim Pharma, Biberach an der Riß, Germany
| | - Andreas H Luippold
- Drug Discovery Sciences, Boehringer Ingelheim Pharma, Biberach an der Riß, Germany
| | - Frank H Büttner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma, Biberach an der Riß, Germany
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22
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Häbe TT, Späth C, Schrade S, Jörg W, Süssmuth RD, Bischoff D, Luippold AH. An ultrafast and flexible liquid chromatography/tandem mass spectrometry system paves the way for machine learning driven in vivo sample processing in early drug discovery. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9096. [PMID: 33837598 DOI: 10.1002/rcm.9096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE The low speed and low flexibility of most liquid chromatography/tandem mass spectrometry (LC/MS/MS) approaches in early drug discovery delay sample analysis from routine in vivo studies within the same day. A high-throughput platform for the rapid quantification of drug compounds in various in vivo assays was developed and established in routine bioanalysis. METHODS Automated selection of an efficient and adequate LC method was realized by autonomous sample qualification for ultrafast batch gradients (9 s/sample) or for fast linear gradients (45 s/sample) if samples required chromatography. The hardware and software components of our Rapid and Integrated Analysis System (RIAS) were streamlined for increased analytical throughput via state-of-the-art automation while maintaining high analytical quality. RESULTS Online decision-making was based on a quick assay suitability test (AST), based on a small and dedicated sample set evaluated by two different strategies. 84% of the acquired data points were within ±30% accuracy and 93% of the deviations between the lower limit of quantitation (LLOQ) values were ≤2-fold compared with standard LC/MS/MS systems. Speed, flexibility and overall automation significantly improved. CONCLUSIONS The developed platform provided an analysis time of only 10 min (batch-mode) and 47 min (gradient-mode) per standard pharmacokinetic (PK) study (62 injections). Automation, data evaluation and results handling were optimized to pave the way for machine learning based on decision-making regarding the evaluation strategy of the AST.
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Affiliation(s)
- Tim T Häbe
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
| | - Christian Späth
- Boehringer Ingelheim Pharma GmbH & Co. KG, ISEE Infrastructure, Safety, Environment and Engineering, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
| | - Steffen Schrade
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
| | - Wolfgang Jörg
- Boehringer Ingelheim Pharma GmbH & Co. KG, ISEE Infrastructure, Safety, Environment and Engineering, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, Berlin, 10623, Germany
| | - Daniel Bischoff
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
| | - Andreas H Luippold
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, Biberach an der Riss, 88397, Germany
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23
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Pu F, Radosevich AJ, Sawicki JW, Chang-Yen D, Talaty NN, Gopalakrishnan SM, Williams JD, Elsen NL. High-Throughput Label-Free Biochemical Assays Using Infrared Matrix-Assisted Desorption Electrospray Ionization Mass Spectrometry. Anal Chem 2021; 93:6792-6800. [PMID: 33885291 DOI: 10.1021/acs.analchem.1c00737] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mass spectrometry (MS) can provide high sensitivity and specificity for biochemical assays without the requirement of labels, eliminating the risk of assay interference. However, its use had been limited to lower-throughput assays due to the need for chromatography to overcome ion suppression from the sample matrix. Direct analysis without chromatography has the potential for high throughput if sensitivity is sufficient despite the presence of a matrix. Here, we report and demonstrate a novel direct analysis high-throughput MS system based on infrared matrix-assisted desorption electrospray ionization (IR-MALDESI) that has a potential acquisition rate of 33 spectra/s. We show the development of biochemical assays in standard buffers for wild-type isocitrate dehydrogenase 1 (IDH1), diacylglycerol kinase zeta (DGKζ), and p300 histone acetyltransferase (P300) to demonstrate the suitability of this system for a broad range of high-throughput lead discovery assays. A proof-of-concept pilot screen of ∼3k compounds is also shown for IDH1 and compared to a previously reported fluorescence-based assay. We were able to obtain reliable data at a speed amenable for high-throughput screening of large-scale compound libraries.
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Affiliation(s)
- Fan Pu
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Andrew J Radosevich
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - James W Sawicki
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - David Chang-Yen
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Nari N Talaty
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Sujatha M Gopalakrishnan
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Jon D Williams
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Nathaniel L Elsen
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
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24
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Wen X, Liu C, Ghislain L, Tovar K, Shah V, Stout SJ, Cifelli S, Satapati S, O’Donnell G, Sheth PR, Wildey MJ, Datwani SS, Covey TR, Bateman KP, McLaren DG. Direct Analysis from Phase-Separated Liquid Samples using ADE-OPI-MS: Applicability to High-Throughput Screening for Inhibitors of Diacylglycerol Acyltransferase 2. Anal Chem 2021; 93:6071-6079. [DOI: 10.1021/acs.analchem.0c04312] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xiujuan Wen
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Chang Liu
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Lucien Ghislain
- Beckman Coulter Life Sciences Incorporated, 170 Rose Orchard Way, San Jose, California 95134, United States
| | - Kiersten Tovar
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Vinit Shah
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Steven J. Stout
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Steven Cifelli
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Santhosh Satapati
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Gregory O’Donnell
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Payal R. Sheth
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Mary Jo Wildey
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Sammy S. Datwani
- Beckman Coulter Life Sciences Incorporated, 170 Rose Orchard Way, San Jose, California 95134, United States
| | - Thomas R. Covey
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Kevin P. Bateman
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - David G. McLaren
- Merck & Company, Incorporated, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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25
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Scholle MD, Gurard-Levin ZA. Development of a Novel Label-Free and High-Throughput Arginase-1 Assay Using Self-Assembled Monolayer Desorption Ionization Mass Spectrometry. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:775-782. [PMID: 33754845 DOI: 10.1177/24725552211000677] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Arginase-1, an enzyme that catalyzes the reaction of L-arginine to L-ornithine, is implicated in the tumor immune response and represents an interesting therapeutic target in immuno-oncology. Initiating arginase drug discovery efforts remains a challenge due to a lack of suitable high-throughput assay methodologies. This report describes the combination of self-assembled monolayers and matrix-assisted laser desorption ionization mass spectrometry to enable the first label-free and high-throughput assay for arginase activity. The assay was optimized for kinetically balanced conditions and miniaturized, while achieving a robust assay (Z-factor > 0.8) and a significant assay window [signal-to-background ratio > 20] relative to fluorescent approaches. To validate the assay, the inhibition of the reference compound nor-NOHA (Nω-hydroxy-nor-L-arginine) was evaluated, and the IC50 measured to be in line with reported results (IC50 = 180 nM). The assay was then used to complete a screen of 175,000 compounds, demonstrating the high-throughput capacity of the approach. The label-free format also eliminates opportunities for false-positive results due to interference from library compounds and optical readouts. The assay methodology described here enables new opportunities for drug discovery for arginase and, due to the assay flexibility, can be more broadly applicable for measuring other amino acid-metabolizing enzymes.
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26
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McLaren DG, Shah V, Wisniewski T, Ghislain L, Liu C, Zhang H, Saldanha SA. High-Throughput Mass Spectrometry for Hit Identification: Current Landscape and Future Perspectives. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:168-191. [PMID: 33482074 DOI: 10.1177/2472555220980696] [Citation(s) in RCA: 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.
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27
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Rampler E, Abiead YE, Schoeny H, Rusz M, Hildebrand F, Fitz V, Koellensperger G. Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics-Standardization, Coverage, and Throughput. Anal Chem 2021; 93:519-545. [PMID: 33249827 PMCID: PMC7807424 DOI: 10.1021/acs.analchem.0c04698] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Evelyn Rampler
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Yasin El Abiead
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Harald Schoeny
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Mate Rusz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Institute of Inorganic
Chemistry, University of Vienna, Währinger Straße 42, 1090 Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Veronika Fitz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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28
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Sahasrabuddhe A, Oakley D, Chen K, McCarter JD. Development of a High-Throughput Affinity Mass Spectrometry (AMS) Platform Using Laser Diode Thermal Desorption Ionization Coupled to Mass Spectrometry (LDTD-MS). SLAS DISCOVERY 2020; 26:230-241. [PMID: 33334237 DOI: 10.1177/2472555220979596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Affinity selection mass spectrometry (MS) or, simply, affinity mass spectrometry (AMS) is a label-free technology that has been used to identify high-affinity ligands of target proteins of interest by screening against small-molecule compound libraries and identifying molecules that are enriched in the presence of the target protein. We have previously applied Agilent Technology's (Santa Clara, CA) RapidFire solid-phase extraction (SPE)-based high-throughput MS technology to screen small-molecule libraries using AMS. However, SPE-based technologies rely on fluidics for desalting and separation prior to mass analysis with attendant high solvent consumption, relatively high sample volume requirements, risk of sample carryover, and frequent maintenance. To address these challenges, we have established an AMS platform using a laser diode thermal desorption-atmospheric pressure chemical ionization (LDTD-APCI) ionization source (Phytronix, Quebec, Canada) coupled with a SCIEX 5600+ TripleTOF MS (Framingham, MA). We also validated a data-independent acquisition (DIA) Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) method for the robust detection and analysis of small-molecule affinity hits. An informatics platform developed in-house has resulted in a streamlined data analysis workflow for high-throughput AMS screening campaigns and reduced data processing time without compromising data quality. Finally, 68,000 compounds were screened in a single plate and affinity selected hits were confirmed in an orthogonal enzyme activity assay.
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Affiliation(s)
| | - Dylan Oakley
- Research Automation Technologies, Thousand Oaks, CA, USA
| | - Kui Chen
- Discovery Technologies, Thousand Oaks, CA, USA
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29
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Pu F, Elsen NL, Williams JD. Emerging Chromatography-Free High-Throughput Mass Spectrometry Technologies for Generating Hits and Leads. ACS Med Chem Lett 2020; 11:2108-2113. [PMID: 33214819 PMCID: PMC7667647 DOI: 10.1021/acsmedchemlett.0c00314] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022] Open
Abstract
Mass spectrometry (MS) detection can offer unmatched selectivity and sensitivity. The use of MS without chromatography greatly increases the throughput, making it suitable for high throughput screening. However, the trade-offs of direct MS detection need to be carefully evaluated along with the development of novel strategies to ensure successful implementation. In this review, we will discuss the pros and cons of chromatography-free MS and discuss some of the currently used and future technologies being investigated to enable high-throughput MS.
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Affiliation(s)
- Fan Pu
- Drug Discovery Science and Technology, AbbVie Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Nathaniel L. Elsen
- Drug Discovery Science and Technology, AbbVie Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Jon D. Williams
- Drug Discovery Science and Technology, AbbVie Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
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30
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De Cesare V, Moran J, Traynor R, Knebel A, Ritorto MS, Trost M, McLauchlan H, Hastie CJ, Davies P. High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry-based deubiquitylating enzyme assay for drug discovery. Nat Protoc 2020; 15:4034-4057. [PMID: 33139956 DOI: 10.1038/s41596-020-00405-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
Deubiquitylating enzymes (DUBs) play a vital role in the ubiquitin pathway by editing or removing ubiquitin from their substrate. As breakthroughs within the ubiquitin field continue to highlight the potential of deubiquitylating enzymes as drug targets, there is increasing demand for versatile high-throughput (HT) tools for the identification of potent and selective DUB modulators. Here we present the HT adaptation of the previously published MALDI-TOF-based DUB assay method. In a MALDI-TOF DUB assay, we quantitate the amount of mono-ubiquitin generated by the in vitro cleavage of ubiquitin chains by DUBs. The method has been specifically developed for use with nanoliter-dispensing robotics to meet drug discovery requirements for the screening of large and diverse compound libraries. Contrary to the most common DUB screening technologies currently available, the MALDI-TOF DUB assay combines the use of physiological substrates with the sensitivity and reliability of the mass spectrometry-based readout.
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Affiliation(s)
- Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.
| | - Jennifer Moran
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Ryan Traynor
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
| | - Maria Stella Ritorto
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.,Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, UK
| | - Hilary McLauchlan
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.
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31
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Simon RP, Winter M, Kleiner C, Wehrle L, Karnath M, Ries R, Zeeb M, Schnapp G, Fiegen D, Häbe TT, Runge F, Bretschneider T, Luippold AH, Bischoff D, Reindl W, Büttner FH. MALDI-TOF-Based Affinity Selection Mass Spectrometry for Automated Screening of Protein-Ligand Interactions at High Throughput. SLAS DISCOVERY 2020; 26:44-57. [PMID: 33073664 DOI: 10.1177/2472555220959266] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Demonstration of in vitro target engagement for small-molecule ligands by measuring binding to a molecular target is an established approach in early drug discovery and a pivotal step in high-throughput screening (HTS)-based compound triaging. We describe the setup, evaluation, and application of a ligand binding assay platform combining automated affinity selection (AS)-based sample preparation and label-free matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis. The platform enables mass spectrometry (MS)-based HTS for small-molecule target interactions from single-compound incubation mixtures and is embedded into a regular assay automation environment. Efficient separation of target-ligand complexes is achieved by in-plate size exclusion chromatography (SEC), and small-molecule ligands are subsequently identified by MALDI-TOF analysis. In contrast to alternative HTS-capable binding assay formats, MALDI-TOF AS-MS is capable of identifying orthosteric and allosteric ligands, as shown for the model system protein tyrosine phosphatase 1B (PTP1B), irrespective of protein function. Furthermore, determining relative binding affinities (RBAs) enabled ligand ranking in accordance with functional inhibition and reference data for PTP1B and a number of diverse protein targets. Finally, we present a validation screen of more than 23,000 compounds within 24 h, demonstrating the general applicability of the platform for the HTS-compatible assessment of protein-ligand interactions.
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Affiliation(s)
- Roman P Simon
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Martin Winter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Carola Kleiner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Lucie Wehrle
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Michael Karnath
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Robert Ries
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Markus Zeeb
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Gisela Schnapp
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Dennis Fiegen
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Tim T Häbe
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Frank Runge
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Tom Bretschneider
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Andreas H Luippold
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Daniel Bischoff
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Wolfgang Reindl
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Frank H Büttner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
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32
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Cramer R. High-speed Analysis of Large Sample Sets - How Can This Key Aspect of the Omics Be Achieved? Mol Cell Proteomics 2020; 19:1760-1766. [PMID: 32796012 DOI: 10.1074/mcp.p120.001997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/29/2020] [Indexed: 01/25/2023] Open
Abstract
High-speed analysis of large (prote)omics sample sets at the rate of thousands or millions of samples per day on a single platform has been a challenge since the beginning of proteomics. For many years, ESI-based MS methods have dominated proteomics because of their high sensitivity and great depth in analyzing complex proteomes. However, despite improvements in speed, ESI-based MS methods are fundamentally limited by their sample introduction, which excludes off-line sample preparation/fractionation because of the time required to switch between individual samples/sample fractions, and therefore being dependent on the speed of on-line sample preparation methods such as liquid chromatography. Laser-based ionization methods have the advantage of moving from one sample to the next without these limitations, being mainly restricted by the speed of modern sample stages, i.e. 10 ms or less between samples. This speed matches the data acquisition speed of modern high-performing mass spectrometers whereas the pulse repetition rate of the lasers (>1 kHz) provides a sufficient number of desorption/ionization events for successful ion signal detection from each sample at the above speed of the sample stages. Other advantages of laser-based ionization methods include the generally higher tolerance to sample additives and contamination compared with ESI MS, and the contact-less and pulsed nature of the laser used for desorption, reducing the risk of cross-contamination. Furthermore, new developments in MALDI have expanded its analytical capabilities, now being able to fully exploit high-performing hybrid mass analyzers and their strengths in sensitivity and MS/MS analysis by generating an ESI-like stable yield of multiply charged analyte ions. Thus, these new developments and the intrinsically high speed of laser-based methods now provide a good basis for tackling extreme sample analysis speed in the omics.
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Affiliation(s)
- Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK.
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33
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Häbe TT, Liu C, Covey TR, Simon RP, Reindl W, Büttner FH, Winter M, Bischoff D, Luippold AH, Runge F. Ultrahigh-Throughput ESI-MS: Sampling Pushed to Six Samples per Second by Acoustic Ejection Mass Spectrometry. Anal Chem 2020; 92:12242-12249. [DOI: 10.1021/acs.analchem.0c01632] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Tim T. Häbe
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Chang Liu
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Tom R. Covey
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Roman P. Simon
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Wolfgang Reindl
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Frank H. Büttner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Martin Winter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Daniel Bischoff
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Andreas H. Luippold
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Frank Runge
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
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34
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Krenkel H, Hartmane E, Piras C, Brown J, Morris M, Cramer R. Advancing Liquid Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Toward Ultrahigh-Throughput Analysis. Anal Chem 2020; 92:2931-2936. [PMID: 31967792 PMCID: PMC7145281 DOI: 10.1021/acs.analchem.9b05202] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Label-free high-throughput screening using mass spectrometry has the potential to provide rapid large-scale sample analysis at a speed of more than one sample per second. Such speed is important for compound library, assay and future clinical screening of millions of samples within a reasonable time frame. Herein, we present a liquid atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) setup for high-throughput large-scale sample analysis (>5 samples per second) for three substance classes (peptides, antibiotics, and lipids). Liquid support matrices (LSM) were used for the analysis of standard substances as well as complex biological fluids (milk). Throughput and analytical robustness were mainly dependent on the complexity of the sample composition and the current limitations of the commercial hardware. However, the ultimate limits of liquid AP-MALDI in sample throughput can be conservatively estimated to be beyond 10-20 samples per second. This level of analytical speed is highly competitive compared with other label-free MS methods, including electrospray ionization and solid state MALDI, as well as MS methods using multiplexing by labeling, which in principle can also be used in combination with liquid AP-MALDI MS.
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Affiliation(s)
- Henriette Krenkel
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Evita Hartmane
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Cristian Piras
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Jeffery Brown
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom.,Waters Corporation , Stamford Avenue , Wilmslow SK9 4AX , United Kingdom
| | - Michael Morris
- Waters Corporation , Stamford Avenue , Wilmslow SK9 4AX , United Kingdom
| | - Rainer Cramer
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
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35
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Simon RP, Winter M, Kleiner C, Ries R, Schnapp G, Heimann A, Li J, Zuvela-Jelaska L, Bretschneider T, Luippold AH, Reindl W, Bischoff D, Büttner FH. MALDI-TOF Mass Spectrometry-Based High-Throughput Screening for Inhibitors of the Cytosolic DNA Sensor cGAS. SLAS DISCOVERY 2019; 25:372-383. [DOI: 10.1177/2472555219880185] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Comprehensive and unbiased detection methods are a prerequisite for high-throughput screening (HTS) campaigns within drug discovery research. Label-free matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has been introduced as an HTS-compatible readout for biochemical test systems to support the drug discovery process. So far, reported HTS applications were based on surface-modified systems or proof-of-concept studies. We present the utilization of a MALDI-TOF-based screening platform to identify inhibitors of human cyclic GMP-AMP synthase (cGAS), a mediator of innate immune response whose aberration has been causally correlated to a number of inflammatory disorders. In this context, the development and validation of a MALDI-TOF-based activity assay is reported to demonstrate fast, robust, and accurate detection of chemical cGAS inhibition by direct quantification of the physiological reaction product cyclic GMP-ATP (cGAMP). Results from a screen of a diverse library of more than 1 million small molecules in 1536-well format against the catalytic cGAS activity are presented with excellent assay performance and data quality. Identified hits were qualified in dose–response experiments and confirmed by RapidFire-MS measurements. Conclusively, the presented data provide the first proof of applicability of direct automated MALDI-TOF MS as a readout strategy for large-scale drug discovery HTS campaigns.
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Affiliation(s)
- Roman P. Simon
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Martin Winter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Carola Kleiner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Robert Ries
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Gisela Schnapp
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Annekatrin Heimann
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Jun Li
- Immunology & Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
| | - Ljiljana Zuvela-Jelaska
- Immunology & Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
| | - Tom Bretschneider
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Andreas H. Luippold
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Wolfgang Reindl
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Daniel Bischoff
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Frank H. Büttner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
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