1
|
Liu C, Zhang H. Data processing for high-throughput mass spectrometry in drug discovery. Expert Opin Drug Discov 2024; 19:815-825. [PMID: 38785418 DOI: 10.1080/17460441.2024.2354871] [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: 03/25/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
INTRODUCTION High-throughput mass spectrometry that could deliver > 10 times faster sample readout speed than traditional LC-based platforms has emerged as a powerful analytical technique, enabling the rapid analysis of complex biological samples. This increased speed of MS data acquisition has brought a critical demand for automatic data processing capabilities that should match or surpass the speed of data acquisition. Those data processing capabilities should serve the different requirements of drug discovery workflows. AREAS COVERED This paper introduced the key steps of the automatic data processing workflows for high-throughput MS technologies. Specific examples and requirements are detailed for different drug discovery applications. EXPERT OPINION The demand for automatic data processing in high-throughput mass spectrometry is driven by the need to keep pace with the accelerated speed of data acquisition. The seamless integration of processing capabilities with LIMS, efficient data review mechanisms, and the exploration of future features such as real-time feedback, automatic method optimization, and AI model training is crucial for advancing the drug discovery field. As technology continues to evolve, the synergy between high-throughput mass spectrometry and intelligent data processing will undoubtedly play a pivotal role in shaping the future of high-throughput drug discovery applications.
Collapse
Affiliation(s)
| | - Hui Zhang
- Iambic Therapeutics, San Diego, CA, USA
| |
Collapse
|
2
|
Zhou Y, Tan C, Zenobi R. Rapid Profiling of the Glycosylation Effects on the Binding of SARS-CoV-2 Spike Protein to Angiotensin-Converting Enzyme 2 Using MALDI-MS with High Mass Detection. Anal Chem 2024; 96:1898-1905. [PMID: 38279913 DOI: 10.1021/acs.analchem.3c03930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
The spike protein receptor-binding domain (RBD) of SARS-CoV-2 binds directly to angiotensin-converting enzyme 2 (ACE2), mediating the host cell entry of SARS-CoV-2. Both spike protein and ACE2 are highly glycosylated, which can regulate the binding. Here, we utilized high-mass MALDI-MS with chemical cross-linking for profiling the glycosylation effects on the binding between RBD and ACE2. Overall, it was found that ACE2 glycosylation affects the binding more strongly than does RBD glycosylation. The binding affinity was improved after desialylation or partial deglycosylation (N690) of ACE2, while it decreased after degalactosylation. ACE2 can form dimers in solution, which bind more tightly to the RBD than the ACE2 monomers. The ACE2 dimerization and the binding of RBD to dimeric ACE2 can also be improved by the desialylation or deglycosylation of ACE2. Partial deglycosylation of ACE2 increased the dimerization of ACE2 and the binding affinity of RBD and ACE2 by more than a factor of 2, suggesting its high potential for neutralizing SARS-CoV-2. The method described in the work provided a simple way to analyze the protein-protein interaction without sample purification. It can be widely used for rapid profiling of glycosylation effects on protein-protein interaction for glycosylation-related diseases and the study of multiple interactions between protein and protein aggregates in a single system.
Collapse
Affiliation(s)
- Yuye Zhou
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), CH-8093 Zürich, Switzerland
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Chemistry, Division of Applied Physical Chemistry, Analytical Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Congrui Tan
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), CH-8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), CH-8093 Zürich, Switzerland
| |
Collapse
|
3
|
Pirrone GF, Munsell EV, Ferguson HM, Al-Sayah MA, Luthra SA, Makarov AA. Automated High-Throughput Matrix Assisted Laser Desorption Ionization Mass Spectrometry Methodology for Formulation Assessment of Polyethylene-Glycol-Conjugated Cytokine Proteins. J Pharm Sci 2023; 112:2778-2782. [PMID: 37478972 DOI: 10.1016/j.xphs.2023.07.013] [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: 02/07/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Biological therapeutics are major contributors to the pharmaceutical pipeline and continue to grow in sales and scope. Additionally, the field's understanding of cancer biology has advanced such that biopharmaceuticals can harness the power of the immune system for oncology treatments. Several of these novel therapeutics are engineered versions of naturally occurring proteins designed to improve therapeutic properties including potency, target engagement and half-life extension. Cytokines, such as interferons and interleukins, are a broad class of signaling proteins which modulate the body's immune response; engineered cytokines have entered the clinic as promising new immuno-oncology therapies. While these therapies hold great promise, their additional structural complexity introduces analytical challenges, and traditional analytical platforms may be ill-suited to effectively assess product development risks. Further, the pharmaceutical industry relies on streamlining approaches for high-throughput experimentation to achieve speed and efficiency for the discovery and development of new modalities. These demands necessitate the use of state-of-the-art techniques to rapidly characterize these new modalities and guide process development and optimization. Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) is a rapid, sensitive and automatable technique amenable for high-throughput analysis of proteins. In this work, we have developed an automated MALDI-MS platform to prepare, acquire and analyze molecular degradation in engineered PEGylated cytokines formulation samples. This orthogonal technique integrated seamlessly with current developability risk assessment workflows, ultimately enabling selection of a final formulation strategy for clinical development.
Collapse
Affiliation(s)
- Gregory F Pirrone
- Merck & Co., Inc., Analytical Research & Development, 33 Avenue Louis Pasteur, Boston, MA, USA.
| | - Erik V Munsell
- Merck & Co., Inc., Discovery Pharmaceutical Sciences, 33 Avenue Louis Pasteur, Boston, MA, USA
| | - Heidi M Ferguson
- Merck & Co., Inc., Discovery Pharmaceutical Sciences, 33 Avenue Louis Pasteur, Boston, MA, USA
| | - Mohammad A Al-Sayah
- Merck & Co., Inc., Analytical Research & Development, 33 Avenue Louis Pasteur, Boston, MA, USA
| | - Suman A Luthra
- Merck & Co., Inc., Discovery Pharmaceutical Sciences, 33 Avenue Louis Pasteur, Boston, MA, USA
| | - Alexey A Makarov
- Merck & Co., Inc., Analytical Research & Development, 33 Avenue Louis Pasteur, Boston, MA, USA.
| |
Collapse
|
4
|
Arciniega C, Garrard KP, Guymon JP, Manni JG, Apffel A, Fjeldsted JC, Muddiman DC. Quasi-continuous infrared matrix-assisted laser desorption electrospray ionization source coupled to a quadrupole time-of-flight mass spectrometer for direct analysis from well plates. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4902. [PMID: 36694312 PMCID: PMC9944147 DOI: 10.1002/jms.4902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/03/2022] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
High-throughput screening (HTS) is a technique mostly used by pharmaceutical companies to rapidly screen multiple libraries of compounds to find drug hits with biological or pharmaceutical activity. Mass spectrometry (MS) has become a popular option for HTS given that it can simultaneously resolve hundreds to thousands of compounds without additional chemical derivatization. For this application, it is convenient to do direct analysis from well plates. Herein, we present the development of an infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) source coupled directly to an Agilent 6545 for direct analysis from well plates. The source is coupled to a quadrupole time-of-flight (Q-TOF) mass spectrometer to take advantage of the high acquisition rates without sacrificing resolving power as required with Orbitrap or Fourier-transform ion cyclotron resonance (FTICR) instruments. The laser used for this source operates at 100 Hz, firing 1 pulse-per-burst, and delivers around 0.7 mJ per pulse. Continuously firing this laser for an extended duration makes it a quasi-continuous ionization source. Additionally, a metal capillary was constructed to extend the inlet of the mass spectrometer, increase desolvation of electrospray charged droplets, improve ion transmission, and increase sensitivity. Its efficiency was compared with the conventional dielectric glass capillary by measured signal and demonstrated that the metal capillary increased ionization efficiency due to its more uniformly distributed temperature gradient. Finally, we present the functionality of the source by analyzing tune mix directly from well plates. This source is a proof of concept for HTS applications using IR-MALDESI coupled to a different MS platform.
Collapse
Affiliation(s)
- Cristina Arciniega
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNC27695USA
| | - Kenneth P. Garrard
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNC27695USA
- Precision Engineering ConsortiumNorth Carolina State UniversityRaleighNC27695USA
- Molecular Education, Technology and Research Innovation Center (METRIC)North Carolina State UniversityRaleighNC27695USA
| | - Jacob P. Guymon
- Precision Engineering ConsortiumNorth Carolina State UniversityRaleighNC27695USA
| | | | | | | | - David C. Muddiman
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNC27695USA
- Molecular Education, Technology and Research Innovation Center (METRIC)North Carolina State UniversityRaleighNC27695USA
| |
Collapse
|
5
|
Dueñas ME, Peltier‐Heap RE, Leveridge M, Annan RS, Büttner FH, Trost M. Advances in high-throughput mass spectrometry in drug discovery. EMBO Mol Med 2022; 15:e14850. [PMID: 36515561 PMCID: PMC9832828 DOI: 10.15252/emmm.202114850] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 12/15/2022] Open
Abstract
High-throughput (HT) screening drug discovery, during which thousands or millions of compounds are screened, remains the key methodology for identifying active chemical matter in early drug discovery pipelines. Recent technological developments in mass spectrometry (MS) and automation have revolutionized the application of MS for use in HT screens. These methods allow the targeting of unlabelled biomolecules in HT assays, thereby expanding the breadth of targets for which HT assays can be developed compared to traditional approaches. Moreover, these label-free MS assays are often cheaper, faster, and more physiologically relevant than competing assay technologies. In this review, we will describe current MS techniques used in drug discovery and explain their advantages and disadvantages. We will highlight the power of mass spectrometry in label-free in vitro assays, and its application for setting up multiplexed cellular phenotypic assays, providing an exciting new tool for screening compounds in cell lines, and even primary cells. Finally, we will give an outlook on how technological advances will increase the future use and the capabilities of mass spectrometry in drug discovery.
Collapse
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
| |
Collapse
|
6
|
Marín-Rubio JL, Peltier-Heap RE, Dueñas ME, Heunis T, Dannoura A, Inns J, Scott J, Simpson AJ, Blair HJ, Heidenreich O, Allan JM, Watt JE, Martin MP, Saxty B, Trost M. A Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Assay Identifies Nilotinib as an Inhibitor of Inflammation in Acute Myeloid Leukemia. J Med Chem 2022; 65:12014-12030. [PMID: 36094045 PMCID: PMC9511480 DOI: 10.1021/acs.jmedchem.2c00671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Inflammatory responses are important in cancer, particularly
in the context of monocyte-rich aggressive myeloid neoplasm. We developed
a label-free cellular phenotypic drug discovery assay to identify
anti-inflammatory drugs in human monocytes derived from acute myeloid
leukemia (AML), by tracking several features ionizing from only 2500
cells using matrix-assisted laser desorption/ionization-time of flight
(MALDI-TOF) mass spectrometry. A proof-of-concept screen showed that
the BCR-ABL inhibitor nilotinib, but not the structurally similar
imatinib, blocks inflammatory responses. In order to identify the
cellular (off-)targets of nilotinib, we performed thermal proteome
profiling (TPP). Unlike imatinib, nilotinib and other later-generation
BCR-ABL inhibitors bind to p38α and inhibit the p38α-MK2/3
signaling axis, which suppressed pro-inflammatory cytokine expression,
cell adhesion, and innate immunity markers in activated monocytes
derived from AML. Thus, our study provides a tool for the discovery
of new anti-inflammatory drugs, which could contribute to the treatment
of inflammation in myeloid neoplasms and other diseases.
Collapse
Affiliation(s)
- José Luis Marín-Rubio
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Rachel E Peltier-Heap
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Maria Emilia Dueñas
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Tiaan Heunis
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Abeer Dannoura
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Joseph Inns
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Jonathan Scott
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - A John Simpson
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK.,Respiratory Medicine Unit, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Helen J Blair
- Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Olaf Heidenreich
- Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - James M Allan
- Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Jessica E Watt
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Mathew P Martin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Barbara Saxty
- LifeArc, SBC Open Innovation Campus, Stevenage SG1 2FX, UK
| | - Matthias Trost
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| |
Collapse
|
7
|
Campbell RM. The SLAS Discovery Editor's Top 10 for 2021. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:77-78. [PMID: 35104635 DOI: 10.1016/j.slasd.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
|
8
|
Hanna GS, Choo YM, Harbit R, Paeth H, Wilde S, Mackle J, Verga JU, Wolf BJ, Thomas OP, Croot P, Cray J, Thomas C, Li LZ, Hardiman G, Hu JF, Wang X, Patel D, Schinazi RF, O’Keefe BR, Hamann MT. Contemporary Approaches to the Discovery and Development of Broad-Spectrum Natural Product Prototypes for the Control of Coronaviruses. JOURNAL OF NATURAL PRODUCTS 2021; 84:3001-3007. [PMID: 34677966 PMCID: PMC8547502 DOI: 10.1021/acs.jnatprod.1c00625] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 05/25/2023]
Abstract
The pressing need for SARS-CoV-2 controls has led to a reassessment of strategies to identify and develop natural product inhibitors of zoonotic, highly virulent, and rapidly emerging viruses. This review article addresses how contemporary approaches involving computational chemistry, natural product (NP) and protein databases, and mass spectrometry (MS) derived target-ligand interaction analysis can be utilized to expedite the interrogation of NP structures while minimizing the time and expense of extraction, purification, and screening in BioSafety Laboratories (BSL)3 laboratories. The unparalleled structural diversity and complexity of NPs is an extraordinary resource for the discovery and development of broad-spectrum inhibitors of viral genera, including Betacoronavirus, which contains MERS, SARS, SARS-CoV-2, and the common cold. There are two key technological advances that have created unique opportunities for the identification of NP prototypes with greater efficiency: (1) the application of structural databases for NPs and target proteins and (2) the application of modern MS techniques to assess protein-ligand interactions directly from NP extracts. These approaches, developed over years, now allow for the identification and isolation of unique antiviral ligands without the immediate need for BSL3 facilities. Overall, the goal is to improve the success rate of NP-based screening by focusing resources on source materials with a higher likelihood of success, while simultaneously providing opportunities for the discovery of novel ligands to selectively target proteins involved in viral infection.
Collapse
Affiliation(s)
- George S. Hanna
- Departments of Drug Discovery and Biomedical Sciences and Public Health, Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Yeun-Mun Choo
- Department of Chemistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Ryan Harbit
- College of Charleston, Charleston, South Carolina 29425, United States
| | - Heather Paeth
- Departments of Drug Discovery and Biomedical Sciences and Public Health, Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Sarah Wilde
- Department of Biology, Clemson University, Clemson, South Carolina 29631, United States
| | - James Mackle
- School of Biological Sciences & Institute for Global Food Security, Queens University, Belfast, Northern Ireland, United Kingdom
| | - Jacopo-Umberto Verga
- School of Biological Sciences & Institute for Global Food Security, Queens University, Belfast, Northern Ireland, United Kingdom
| | - Bethany J. Wolf
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Olivier P. Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway, Galway H91Tk33, Ireland
| | - Peter Croot
- Irish Centre for Research in Applied Geoscience, Earth and Ocean Sciences and Ryan Institute, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland
| | - James Cray
- Department of Biomedical Education and Anatomy, College of Medicine and Division of Biosciences, College of Dentistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Courtney Thomas
- Department of Chemistry, South Carolina State University, Orangeburg, South Carolina, United States
| | - Ling-Zhi Li
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University/SPU, Shenyang, China
| | - Gary Hardiman
- School of Biological Sciences & Institute for Global Food Security, Queens University, Belfast, Northern Ireland, United Kingdom
| | - Jin-Feng Hu
- School of Advanced Study, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang 318000, China
| | - Xiaojuan Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Dharmeshkhumar Patel
- Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine, and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Raymond F. Schinazi
- Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine, and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Barry R. O’Keefe
- Molecular Targets Program, Center for Cancer Research, Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Mark T. Hamann
- Departments of Drug Discovery and Biomedical Sciences and Public Health, Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| |
Collapse
|
9
|
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.
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
McLaren DG, Shah V, Wisniewski T, Ghislain L, Liu C, Zhang H, Saldanha SA. High-Throughput Mass Spectrometry for Hit Identification: Current Landscape and Future Perspectives. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:168-191. [PMID: 33482074 DOI: 10.1177/2472555220980696] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
For nearly two decades mass spectrometry has been used as a label-free, direct-detection method for both functional and affinity-based screening of a wide range of therapeutically relevant target classes. Here, we present an overview of several established and emerging mass spectrometry platforms and summarize the unique strengths and performance characteristics of each as they apply to high-throughput screening. Multiple examples from the recent literature are highlighted in order to illustrate the power of each individual technique, with special emphasis given to cases where the use of mass spectrometry was found to be differentiating when compared with other detection formats. Indeed, as many of these examples will demonstrate, the inherent strengths of mass spectrometry-sensitivity, specificity, wide dynamic range, and amenability to complex matrices-can be leveraged to enhance the discriminating power and physiological relevance of assays included in screening cascades. It is our hope that this review will serve as a useful guide to readers of all backgrounds and experience levels on the applicability and benefits of mass spectrometry in the search for hits, leads, and, ultimately, drugs.
Collapse
|