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Seal S, Trapotsi MA, Spjuth O, Singh S, Carreras-Puigvert J, Greene N, Bender A, Carpenter AE. A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592531. [PMID: 38766203 PMCID: PMC11100607 DOI: 10.1101/2024.05.04.592531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions. Here, we systematically review the substantial methodological advancements and applications of Cell Painting. Advancements include improvements in the Cell Painting protocol, assay adaptations for different types of perturbations and applications, and improved methodologies for feature extraction, quality control, and batch effect correction. Moreover, machine learning methods recently surpassed classical approaches in their ability to extract biologically useful information from Cell Painting images. Cell Painting data have been used alone or in combination with other - omics data to decipher the mechanism of action of a compound, its toxicity profile, and many other biological effects. Overall, key methodological advances have expanded Cell Painting's ability to capture cellular responses to various perturbations. Future advances will likely lie in advancing computational and experimental techniques, developing new publicly available datasets, and integrating them with other high-content data types.
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Affiliation(s)
- Srijit Seal
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Maria-Anna Trapotsi
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Shantanu Singh
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Jordi Carreras-Puigvert
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Nigel Greene
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Andreas Bender
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Anne E. Carpenter
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
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Garcia MB, Singh M, Miller E, Neuenswander S, Douglas J, Boskovic Z. Twisted Intramolecular Charge-Transfer State Addition to Electron-Poor Olefins. J Org Chem 2024; 89:3058-3064. [PMID: 38354334 PMCID: PMC11006016 DOI: 10.1021/acs.joc.3c02521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
When electron-rich arylpyrrolinium salts are irradiated with ultraviolet light in the presence of Michael acceptors, the pyrrolinyl and aryl fragments add to the activated and polarized double bond in a regioselective manner, forming two C-C bonds and fragmenting the substrate. In this paper, we present a model for this intriguing reaction, supported by spectroscopy and computational analyses, and provide evidence for rectifying previously misassigned structures. We postulate that the photochemical reaction is inefficient because the reaction between the twisted intramolecular charge-transfer state and the olefin competes with fluorescence from this state upon photon absorption. We also discuss the practical advantages of performing this photochemical reaction in a continuous flow setup. Additionally, we explore several subsequent reactions that allow us to further modify the products of the photochemical step, ultimately leading to the creation of new chemical structures.
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Affiliation(s)
- Mauricio Bahena Garcia
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Manvendra Singh
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Elizabeth Miller
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Sarah Neuenswander
- Nuclear Magnetic Resonance Laboratory, University of Kansas, Lawrence, Kansas 66045, United States
| | - Justin Douglas
- Nuclear Magnetic Resonance Laboratory, University of Kansas, Lawrence, Kansas 66045, United States
| | - Zarko Boskovic
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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Kolluru S, Singh M, Gaskins B, Boskovic Z. Nickel-Catalyzed Annulations of ortho-Haloarylimines. ACS Catal 2021; 11:10351-10361. [PMID: 34777907 DOI: 10.1021/acscatal.1c03092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the discovery, development, and mechanism of a nickel-catalyzed annulation reaction between o-haloarylimines and electron-poor olefins. The reaction produces two adjacent anti stereocenters and a free secondary amine. Spirocycles are formed from cyclic imines. We characterized the key oxidative addition intermediate and identified a major path leading to competing homocoupling products. The activation energy of oxidative addition and the rate of oxidative addition complex isomerization were determined. The sensitivity of the reaction to reaction conditions was established in a quantitative manner and both the scope and limitations of the method are presented.
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Affiliation(s)
- Srinivas Kolluru
- Department of Medicinal Chemistry, University of Kansas, Lawrence 66045, Kansas
| | - Manvendra Singh
- Department of Medicinal Chemistry, University of Kansas, Lawrence 66045, Kansas
| | - Bryce Gaskins
- Department of Medicinal Chemistry, University of Kansas, Lawrence 66045, Kansas
| | - Zarko Boskovic
- Department of Medicinal Chemistry, University of Kansas, Lawrence 66045, Kansas
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Miki Y, Tomita N, Ban K, Sajiki H, Sawama Y. Synthesis of 1‐Pyrroline by Denitrogenative Ring Expansion of Cyclobutyl Azides under Thermal Conditions. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yuya Miki
- Laboratory of Organic Chemistry Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196, Japan
| | - Naohito Tomita
- Laboratory of Organic Chemistry Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196, Japan
| | - Kazuho Ban
- Laboratory of Organic Chemistry Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196, Japan
| | - Hironao Sajiki
- Laboratory of Organic Chemistry Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196, Japan
| | - Yoshinari Sawama
- Laboratory of Organic Chemistry Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196, Japan
- Graduate School of Pharmaceutical Sciences Osaka University 1-6 Yamada-oka, Suita Osaka 565-0871 Japan
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