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Subramani C, Sharma G, Chaira T, Barman TK. High content screening strategies for large-scale compound libraries with a focus on high-containment viruses. Antiviral Res 2024; 221:105764. [PMID: 38008193 DOI: 10.1016/j.antiviral.2023.105764] [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: 09/11/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
A majority of viral diseases do not have FDA-approved drugs. The recent outbreaks caused by SARS-CoV-2, monkeypox, and Sudan ebolavirus have exposed the critical need for rapid screening and identification of antiviral compounds against emerging/re-emerging viral pathogens. A high-content screening (HCS) platform is becoming an essential part of the drug discovery process, thanks to developments in image acquisition and analysis. While HCS has several advantages, its full potential has not been realized in antiviral drug discovery compared to conventional drug screening approaches, such as fluorescence or luminescence-based microplate assays. Therefore, this review aims to summarize HCS workflow, strategies, and developments in image-based drug screening, focusing on high-containment viruses.
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Affiliation(s)
- Chandru Subramani
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Galveston National Laboratory, Galveston, TX, USA
| | - Ghanshyam Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Tridib Chaira
- Department of Pharmacology, SGT University, Gurugram, Haryana, India
| | - Tarani Kanta Barman
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Galveston National Laboratory, Galveston, TX, USA.
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2
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Peyear TA, Andersen OS. Screening for bilayer-active and likely cytotoxic molecules reveals bilayer-mediated regulation of cell function. J Gen Physiol 2023; 155:e202213247. [PMID: 36763053 PMCID: PMC9948646 DOI: 10.1085/jgp.202213247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/06/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023] Open
Abstract
A perennial problem encountered when using small molecules (drugs) to manipulate cell or protein function is to assess whether observed changes in function result from specific interactions with a desired target or from less specific off-target mechanisms. This is important in laboratory research as well as in drug development, where the goal is to identify molecules that are unlikely to be successful therapeutics early in the process, thereby avoiding costly mistakes. We pursued this challenge from the perspective that many bioactive molecules (drugs) are amphiphiles that alter lipid bilayer elastic properties, which may cause indiscriminate changes in membrane protein (and cell) function and, in turn, cytotoxicity. Such drug-induced changes in bilayer properties can be quantified as changes in the monomer↔dimer equilibrium for bilayer-spanning gramicidin channels. Using this approach, we tested whether molecules in the Pathogen Box (a library of 400 drugs and drug-like molecules with confirmed activity against tropical diseases released by Medicines for Malaria Venture to encourage the development of therapies for neglected tropical diseases) are bilayer modifiers. 32% of the molecules in the Pathogen Box were bilayer modifiers, defined as molecules that at 10 µM shifted the monomer↔dimer equilibrium toward the conducting dimers by at least 50%. Correlation analysis of the molecules' reported HepG2 cell cytotoxicity to bilayer-modifying potency, quantified as the shift in the gramicidin monomer↔dimer equilibrium, revealed that molecules producing <25% change in the equilibrium had significantly lower probability of being cytotoxic than molecules producing >50% change. Neither cytotoxicity nor bilayer-modifying potency (quantified as the shift in the gramicidin monomer↔dimer equilibrium) was well predicted by conventional physico-chemical descriptors (hydrophobicity, polar surface area, etc.). We conclude that drug-induced changes in lipid bilayer properties are robust predictors of the likelihood of membrane-mediated off-target effects, including cytotoxicity.
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Affiliation(s)
- Thasin A. Peyear
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences. New York, NY, USA
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
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Seal S, Yang H, Vollmers L, Bender A. Comparison of Cellular Morphological Descriptors and Molecular Fingerprints for the Prediction of Cytotoxicity- and Proliferation-Related Assays. Chem Res Toxicol 2021; 34:422-437. [PMID: 33522793 DOI: 10.1021/acs.chemrestox.0c00303] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cell morphology features, such as those from the Cell Painting assay, can be generated at relatively low costs and represent versatile biological descriptors of a system and thereby compound response. In this study, we explored cell morphology descriptors and molecular fingerprints, separately and in combination, for the prediction of cytotoxicity- and proliferation-related in vitro assay endpoints. We selected 135 compounds from the MoleculeNet ToxCast benchmark data set which were annotated with Cell Painting readouts, where the relatively small size of the data set is due to the overlap of required annotations. We trained Random Forest classification models using nested cross-validation and Cell Painting descriptors, Morgan and ErG fingerprints, and their combinations. While using leave-one-cluster-out cross-validation (with clusters based on physicochemical descriptors), models using Cell Painting descriptors achieved higher average performance over all assays (Balanced Accuracy of 0.65, Matthews Correlation Coefficient of 0.28, and AUC-ROC of 0.71) compared to models using ErG fingerprints (BA 0.55, MCC 0.09, and AUC-ROC 0.60) and Morgan fingerprints alone (BA 0.54, MCC 0.06, and AUC-ROC 0.56). While using random shuffle splits, the combination of Cell Painting descriptors with ErG and Morgan fingerprints further improved balanced accuracy on average by 8.9% (in 9 out of 12 assays) and 23.4% (in 8 out of 12 assays) compared to using only ErG and Morgan fingerprints, respectively. Regarding feature importance, Cell Painting descriptors related to nuclei texture, granularity of cells, and cytoplasm as well as cell neighbors and radial distributions were identified to be most contributing, which is plausible given the endpoint considered. We conclude that cell morphological descriptors contain complementary information to molecular fingerprints which can be used to improve the performance of predictive cytotoxicity models, in particular in areas of novel structural space.
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Affiliation(s)
- Srijit Seal
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Hongbin Yang
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Luis Vollmers
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Howarth A, Schröder M, Montenegro RC, Drewry DH, Sailem H, Millar V, Müller S, Ebner DV. HighVia-A Flexible Live-Cell High-Content Screening Pipeline to Assess Cellular Toxicity. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:801-811. [PMID: 32458721 PMCID: PMC7522770 DOI: 10.1177/2472555220923979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 02/03/2023]
Abstract
High-content screening to monitor disease-modifying phenotypes upon small-molecule addition has become an essential component of many drug and target discovery platforms. One of the most common phenotypic approaches, especially in the field of oncology research, is the assessment of cell viability. However, frequently used viability readouts employing metabolic proxy assays based on homogeneous colorimetric/fluorescent reagents are one-dimensional, provide limited information, and can in many cases yield conflicting or difficult-to-interpret results, leading to misinterpretation of data and wasted resources.The resurgence of high-content, phenotypic screening has significantly improved the quality and breadth of cell viability data, which can be obtained at the very earliest stages of drug and target discovery. Here, we describe a relatively inexpensive, high-throughput, high-content, multiparametric, fluorescent imaging protocol using a live-cell method of three fluorescent probes (Hoechst, Yo-Pro-3, and annexin V), that is amenable to the addition of further fluorophores. The protocol enables the accurate description and profiling of multiple cell death mechanisms, including apoptosis and necrosis, as well as accurate determination of compound IC50, and has been validated on a range of high-content imagers and image analysis software. To validate the protocol, we have used a small library of approximately 200 narrow-spectrum kinase inhibitors and clinically approved drugs. This fully developed, easy-to-use pipeline has subsequently been implemented in several academic screening facilities, yielding fast, flexible, and rich cell viability data for a range of early-stage high-throughput drug and target discovery programs.
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Affiliation(s)
- Alison Howarth
- Nuffield Department of Clinical Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- These authors contributed equally
| | - Martin Schröder
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Science, Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt, Germany
- These authors contributed equally
| | - Raquel C. Montenegro
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK
- Federal University of Ceará, Drug Research and Development Center (NPDM), Pharmacogenetics Laboratory, Fortaleza, CE, Brazil
- These authors contributed equally
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heba Sailem
- Department of Engineering, University of Oxford, Oxford, UK
| | - Val Millar
- Nuffield Department of Clinical Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Science, Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Daniel V. Ebner
- Nuffield Department of Clinical Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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Twarog C, Liu K, O'Brien PJ, Dawson KA, Fattal E, Illel B, Brayden DJ. A head-to-head Caco-2 assay comparison of the mechanisms of action of the intestinal permeation enhancers: SNAC and sodium caprate (C 10). Eur J Pharm Biopharm 2020; 152:95-107. [PMID: 32387703 DOI: 10.1016/j.ejpb.2020.04.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/15/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023]
Abstract
Salcaprozate sodium (SNAC) and sodium caprate (C10) are the two leading intestinal permeation enhancers (PEs) in oral peptide formulations in clinical trials. There is debate over their mechanism of action on intestinal epithelia. The aims were: (i) to compare their effects on the barrier function by measuring transepithelial electrical resistance (TEER), permeability of FITC-4000 (FD4) across Caco-2 monolayers, and on immunohistochemistry of tight junction (TJ)-associated proteins; and (ii) to compare cellular parameters using conventional end-point cytotoxicity assays and quantitative high content analysis (HCA) of multiple sub-lethal parameters in Caco-2 cells. C10 (8.5 mM) reversibly reduced TEER and increased FD4 permeability across monolayers, whereas SNAC had no effects on either parameter except at cytotoxic concentrations. C10 exposure induced reorganization of three TJ proteins, whereas SNAC only affected claudin-5 localization. High concentrations of C10 and SNAC were required to cause end-point toxicology changes in vitro. SNAC was less potent than C10 at inducing lysosomal and nuclear changes and plasma membrane perturbation. In parallel, HCA revealed that both agents displayed detergent-like features that reflect initial membrane fluidization followed by changes in intracellular parameters. In conclusion, FD4 permeability increases in monolayers in response to C10 were in the range of concentrations that altered end-point cytotoxicity and HCA parameters. For SNAC, while HCA parameters were also altered in a similar overall pattern as C10, they did not lead to increased paracellular flux. These assays show that both agents are primarily surfactants, but C10 has additional TJ-opening effects. While these in vitro assays illucidate their epithelial mechanism of action, clinical experience suggests that they over-estimate their toxicology in the dynamic intestinal environment.
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Affiliation(s)
- Caroline Twarog
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kai Liu
- UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Peter J O'Brien
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kenneth A Dawson
- UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Elias Fattal
- School of Pharmacy, Institut Galien, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Brigitte Illel
- Drug Product Development, Small Molecules Oral Platform, Sanofi Research and Development, Montpellier, France
| | - David J Brayden
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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Lee OW, Austin S, Gamma M, Cheff DM, Lee TD, Wilson KM, Johnson J, Travers J, Braisted JC, Guha R, Klumpp-Thomas C, Shen M, Hall MD. Cytotoxic Profiling of Annotated and Diverse Chemical Libraries Using Quantitative High-Throughput Screening. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:9-20. [PMID: 31498718 PMCID: PMC10791069 DOI: 10.1177/2472555219873068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cell-based phenotypic screening is a commonly used approach to discover biological pathways, novel drug targets, chemical probes, and high-quality hit-to-lead molecules. Many hits identified from high-throughput screening campaigns are ruled out through a series of follow-up potency, selectivity/specificity, and cytotoxicity assays. Prioritization of molecules with little or no cytotoxicity for downstream evaluation can influence the future direction of projects, so cytotoxicity profiling of screening libraries at an early stage is essential for increasing the likelihood of candidate success. In this study, we assessed the cell-based cytotoxicity of nearly 10,000 compounds in the National Institutes of Health, National Center for Advancing Translational Sciences annotated libraries and more than 100,000 compounds in a diversity library against four normal cell lines (HEK 293, NIH 3T3, CRL-7250, and HaCat) and one cancer cell line (KB 3-1, a HeLa subline). This large-scale library profiling was analyzed for overall screening outcomes, hit rates, pan-activity, and selectivity. For the annotated library, we also examined the primary targets and mechanistic pathways regularly associated with cell death. To our knowledge, this is the first study to use high-throughput screening to profile a large screening collection (>100,000 compounds) for cytotoxicity in both normal and cancer cell lines. The results generated here constitute a valuable resource for the scientific community and provide insight into the extent of cytotoxic compounds in screening libraries, allowing for the identification and avoidance of compounds with cytotoxicity during high-throughput screening campaigns.
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Affiliation(s)
- Olivia W. Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Shelley Austin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Madison Gamma
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Dorian M. Cheff
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Tobie D. Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Kelli M. Wilson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Joseph Johnson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jameson Travers
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - John C. Braisted
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Rajarshi Guha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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