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de Jong E, Kocer A. Current Methods for Identifying Plasma Membrane Proteins as Cancer Biomarkers. MEMBRANES 2023; 13:409. [PMID: 37103836 PMCID: PMC10142483 DOI: 10.3390/membranes13040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
Plasma membrane proteins are a special class of biomolecules present on the cellular membrane. They provide the transport of ions, small molecules, and water in response to internal and external signals, define a cell's immunological identity, and facilitate intra- and intercellular communication. Since they are vital to almost all cellular functions, their mutants, or aberrant expression is linked to many diseases, including cancer, where they are a part of cancer cell-specific molecular signatures and phenotypes. In addition, their surface-exposed domains make them exciting biomarkers for targeting by imaging agents and drugs. This review looks at the challenges in identifying cancer-related cell membrane proteins and the current methodologies that solve most of the challenges. We classified the methodologies as biased, i.e., search cells for the presence of already known membrane proteins. Second, we discuss the unbiased methods that can identify proteins without prior knowledge of what they are. Finally, we discuss the potential impact of membrane proteins on the early detection and treatment of cancer.
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2
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Srinivasan B, Flórez Weidinger JD, Zhai X, Lemercier G, Ikeda T, Brewer M, Zhang B, Heyse S, Wingfield J, Steigele S. High-throughput mechanistic screening of non-equilibrium inhibitors by a fully automated data analysis pipeline in early drug-discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:460-470. [PMID: 36156314 DOI: 10.1016/j.slasd.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 12/15/2022]
Abstract
Recent efforts for increasing the success in drug discovery focus on an early, massive, and routine mechanistic and/or kinetic characterization of drug-target engagement as part of a design-make-test-analyze strategy. From an experimental perspective, many mechanistic assays can be translated into a scalable format on automation platforms and thereby enable routine characterization of hundreds or thousands of compounds. However, now the limiting factor to achieve such in-depth characterization at high-throughput becomes the quality-driven data analysis, the sheer scale of which outweighs the time available to the scientific staff of most labs. Therefore, automated analytical workflows are needed to enable such experimental scale-up. We have implemented such a fully automated workflow in Genedata Screener for time-dependent ligand-target binding analysis to characterize non-equilibrium inhibitors. The workflow automates Quality Control (QC) / data modelling and decision-making process in a staged analysis: (1) quality control of raw input data-fluorescence signal-based progress curves - featuring automated rejection of unsuitable measurements; (2) automated model selection - one-step versus two-step binding model - using statistical methods and biological validity rules; (3) result visualization in specific plots and annotated result tables, enabling the scientist to review large result sets efficiently and, at the same time, to rapidly identify and focus on interesting or unusual results; (4) an interactive user interface for immediate adjustment of automated decisions, where necessary. Applying this workflow to first-pass, high-throughput kinetic studies on kinase projects has allowed us to surmount previously rate-limiting manual analysis steps and boost productivity; and is now routinely embedded in a biopharma discovery research process.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK.
| | | | - Xiang Zhai
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Waltham, MA 02451, United States
| | | | - Timothy Ikeda
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Waltham, MA 02451, United States
| | | | - Bairu Zhang
- Data Sciences & Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | - Jonathan Wingfield
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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3
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Application of antibiotic-derived fluorescent probes to bacterial studies. Methods Enzymol 2022; 665:1-28. [DOI: 10.1016/bs.mie.2021.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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4
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Simard JR, Lee L, Vieux E, Improgo R, Tieu T, Phillips AJ, Fisher SL, Pollock RM, Park E. High-Throughput Quantitative Assay Technologies for Accelerating the Discovery and Optimization of Targeted Protein Degradation Therapeutics. SLAS DISCOVERY 2021; 26:503-517. [PMID: 33430712 DOI: 10.1177/2472555220985049] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aberrant regulation of protein expression and function can drastically alter cellular physiology and lead to numerous pathophysiological conditions such as cancer, inflammatory diseases, and neurodegeneration. The steady-state expression levels of endogenous proteins are controlled by a balance of de novo synthesis rates and degradation rates. Moreover, the levels of activated proteins in signaling cascades can be further modulated by a variety of posttranslational modifications and protein-protein interactions. The field of targeted protein degradation is an emerging area for drug discovery in which small molecules are used to recruit E3 ubiquitin ligases to catalyze the ubiquitination and subsequent degradation of disease-causing target proteins by the proteasome in both a dose- and time-dependent manner. Traditional approaches for quantifying protein level changes in cells, such as Western blots, are typically low throughput with limited quantification, making it hard to drive the rapid development of therapeutics that induce selective, rapid, and sustained protein degradation. In the last decade, a number of techniques and technologies have emerged that have helped to accelerate targeted protein degradation drug discovery efforts, including the use of fluorescent protein fusions and reporter tags, flow cytometry, time-resolved fluorescence energy transfer (TR-FRET), and split luciferase systems. Here we discuss the advantages and disadvantages associated with these technologies and their application to the development and optimization of degraders as therapeutics.
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Affiliation(s)
| | - Linda Lee
- C4 Therapeutics, Inc., Watertown, MA, USA
| | | | | | - Trang Tieu
- C4 Therapeutics, Inc., Watertown, MA, USA
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Camacho-Sandoval R, Jiménez-Uribe A, Tenorio-Calvo AV, López-Morales CA, Muñoz-García L, Montes-Luna A, García-Xolalpa HL, Velasco-Velázquez M, Pavón L, Pérez-Tapia SM, Medina-Rivero E. Taking advantage of a high-throughput flow cytometer for the implementation of an ADCC assay for regulatory compliance. ACTA ACUST UNITED AC 2020; 26:e00456. [PMID: 32373484 PMCID: PMC7193121 DOI: 10.1016/j.btre.2020.e00456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 11/19/2022]
Abstract
High-throughput flow cytometry for the evaluation of ADCC potency. Optimization of biological assays for batch release testing of biopharmaceuticals. Quickly turn multi-parameter acquisition by flow cytometry.
Technological advances allowed the development of high-throughput instruments such as IntelliCyt iQue Screener PLUS®. Here, we took advantage of this technology to transfer a previously validated cytotoxicity assay. The evaluated parameters were cell permeability, caspase activation and phosphatidyl serine exposure. The assay was accurate (r2 = 0.90), precise (%CV ≤ 18.90) and specific. These results showed that this technology is suitable to be used in control quality environments. In addition, the automation provided a faster acquisition and analysis of data with precise and accurate results. This application could be implemented to evaluate another in vitro mechanism of action of different biotherapeutics.
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Affiliation(s)
- Rosa Camacho-Sandoval
- Unidad de Desarrollo e Investigación en Bioprocesos. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Alexis Jiménez-Uribe
- Unidad de Desarrollo e Investigación en Bioprocesos. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Alejandra V Tenorio-Calvo
- Unidad de Desarrollo e Investigación en Bioprocesos. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Carlos A López-Morales
- Unidad de Desarrollo e Investigación en Bioprocesos. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Leslie Muñoz-García
- Unidad de Desarrollo e Investigación en Bioprocesos. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Alejandra Montes-Luna
- Unidad de Desarrollo e Investigación en Bioprocesos. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, Ciudad de México, Mexico
| | | | - Marco Velasco-Velázquez
- Departamento de Farmacología y Unidad Periférica de Investigación en Biomedicina Translacional (CMN 20 de noviembre, ISSSTE), Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Lenin Pavón
- Laboratorio de Psicoinmunología. Dirección de Investigaciones en Neurociencias del Instituto Nacional de Psiquiatría, Ciudad de México, Mexico
| | - Sonia Mayra Pérez-Tapia
- Unidad de Desarrollo e Investigación en Bioprocesos. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Emilio Medina-Rivero
- Unidad de Desarrollo e Investigación en Bioprocesos. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, Ciudad de México, Mexico
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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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Rodell CB, Koch PD, Weissleder R. Screening for new macrophage therapeutics. Theranostics 2019; 9:7714-7729. [PMID: 31695796 PMCID: PMC6831478 DOI: 10.7150/thno.34421] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/19/2019] [Indexed: 12/15/2022] Open
Abstract
Myeloid derived macrophages play a key role in many human diseases, and their therapeutic modulation via pharmacological means is receiving considerable attention. Of particular interest is the fact that these cells are i) dynamic phenotypes well suited to therapeutic manipulation and ii) phagocytic, allowing them to be efficiently targeted with nanoformulations. However, it is important to consider that macrophages represent heterogeneous populations of subtypes with often competing biological behaviors and functions. In order to develop next generation therapeutics, it is therefore essential to screen for biological effects through a combination of in vitro and in vivo assays. Here, we review the state-of-the-art techniques, including both cell based screens and in vivo imaging tools that have been developed for assessment of macrophage phenotype. We conclude with a forward-looking perspective on the growing need for noninvasive macrophage assessment and laboratory assays to be put into clinical practice and the potential broader impact of myeloid-targeted therapeutics.
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Friese A, Ursu A, Hochheimer A, Schöler HR, Waldmann H, Bruder JM. The Convergence of Stem Cell Technologies and Phenotypic Drug Discovery. Cell Chem Biol 2019; 26:1050-1066. [PMID: 31231030 DOI: 10.1016/j.chembiol.2019.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 04/04/2019] [Accepted: 05/20/2019] [Indexed: 02/06/2023]
Abstract
Recent advances in induced pluripotent stem cell technologies and phenotypic screening shape the future of bioactive small-molecule discovery. In this review we analyze the impact of small-molecule phenotypic screens on drug discovery as well as on the investigation of human development and disease biology. We further examine the role of 3D spheroid/organoid structures, microfluidic systems, and miniaturized on-a-chip systems for future discovery strategies. In highlighting representative examples, we analyze how recent achievements can translate into future therapies. Finally, we discuss remaining challenges that need to be overcome for the adaptation of the next generation of screening approaches.
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Affiliation(s)
- Alexandra Friese
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Andrei Ursu
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany; Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Andreas Hochheimer
- ISAR Bioscience GmbH, Institute for Stem Cell & Applied Regenerative Medicine Research, 82152 Planegg, Germany
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany; Medical Faculty, University of Münster, Domagkstrasse 3, 48149 Münster, Germany.
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany.
| | - Jan M Bruder
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany.
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9
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Ding M, Edwards BS. High-Throughput Flow Cytometry in Drug Discovery. SLAS DISCOVERY 2018; 23:599-602. [DOI: 10.1177/2472555218778250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Mei Ding
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden
| | - Bruce S. Edwards
- Department of Pathology, Center for Molecular Discovery, University of New Mexico, Albuquerque, NM, USA
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