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Assessing target engagement using proteome-wide solvent shift assays

Recent advances in mass spectrometry (MS) have enabled quantitative proteomics to become a powerful tool in the field of drug discovery, especially when applied toward proteome-wide target engagement studies. Similar to temperature gradients, increasing concentrations of organic solvents stimulate u...

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Autores principales: Van Vranken, Jonathan G, Li, Jiaming, Mitchell, Dylan C, Navarrete-Perea, José, Gygi, Steven P
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8654358/
https://www.ncbi.nlm.nih.gov/pubmed/34878405
http://dx.doi.org/10.7554/eLife.70784
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author Van Vranken, Jonathan G
Li, Jiaming
Mitchell, Dylan C
Navarrete-Perea, José
Gygi, Steven P
author_facet Van Vranken, Jonathan G
Li, Jiaming
Mitchell, Dylan C
Navarrete-Perea, José
Gygi, Steven P
author_sort Van Vranken, Jonathan G
collection PubMed
description Recent advances in mass spectrometry (MS) have enabled quantitative proteomics to become a powerful tool in the field of drug discovery, especially when applied toward proteome-wide target engagement studies. Similar to temperature gradients, increasing concentrations of organic solvents stimulate unfolding and precipitation of the cellular proteome. This property can be influenced by physical association with ligands and other molecules, making individual proteins more or less susceptible to solvent-induced denaturation. Herein, we report the development of proteome-wide solvent shift assays by combining the principles of solvent-induced precipitation (Zhang et al., 2020) with modern quantitative proteomics. Using this approach, we developed solvent proteome profiling (SPP), which is capable of establishing target engagement through analysis of SPP denaturation curves. We readily identified the specific targets of compounds with known mechanisms of action. As a further efficiency boost, we applied the concept of area under the curve analysis to develop solvent proteome integral solubility alteration (solvent-PISA) and demonstrate that this approach can serve as a reliable surrogate for SPP. We propose that by combining SPP with alternative methods, like thermal proteome profiling, it will be possible to increase the absolute number of high-quality melting curves that are attainable by either approach individually, thereby increasing the fraction of the proteome that can be screened for evidence of ligand binding.
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spelling pubmed-86543582021-12-09 Assessing target engagement using proteome-wide solvent shift assays Van Vranken, Jonathan G Li, Jiaming Mitchell, Dylan C Navarrete-Perea, José Gygi, Steven P eLife Biochemistry and Chemical Biology Recent advances in mass spectrometry (MS) have enabled quantitative proteomics to become a powerful tool in the field of drug discovery, especially when applied toward proteome-wide target engagement studies. Similar to temperature gradients, increasing concentrations of organic solvents stimulate unfolding and precipitation of the cellular proteome. This property can be influenced by physical association with ligands and other molecules, making individual proteins more or less susceptible to solvent-induced denaturation. Herein, we report the development of proteome-wide solvent shift assays by combining the principles of solvent-induced precipitation (Zhang et al., 2020) with modern quantitative proteomics. Using this approach, we developed solvent proteome profiling (SPP), which is capable of establishing target engagement through analysis of SPP denaturation curves. We readily identified the specific targets of compounds with known mechanisms of action. As a further efficiency boost, we applied the concept of area under the curve analysis to develop solvent proteome integral solubility alteration (solvent-PISA) and demonstrate that this approach can serve as a reliable surrogate for SPP. We propose that by combining SPP with alternative methods, like thermal proteome profiling, it will be possible to increase the absolute number of high-quality melting curves that are attainable by either approach individually, thereby increasing the fraction of the proteome that can be screened for evidence of ligand binding. eLife Sciences Publications, Ltd 2021-12-08 /pmc/articles/PMC8654358/ /pubmed/34878405 http://dx.doi.org/10.7554/eLife.70784 Text en © 2021, Van Vranken et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Biochemistry and Chemical Biology
Van Vranken, Jonathan G
Li, Jiaming
Mitchell, Dylan C
Navarrete-Perea, José
Gygi, Steven P
Assessing target engagement using proteome-wide solvent shift assays
title Assessing target engagement using proteome-wide solvent shift assays
title_full Assessing target engagement using proteome-wide solvent shift assays
title_fullStr Assessing target engagement using proteome-wide solvent shift assays
title_full_unstemmed Assessing target engagement using proteome-wide solvent shift assays
title_short Assessing target engagement using proteome-wide solvent shift assays
title_sort assessing target engagement using proteome-wide solvent shift assays
topic Biochemistry and Chemical Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8654358/
https://www.ncbi.nlm.nih.gov/pubmed/34878405
http://dx.doi.org/10.7554/eLife.70784
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