Cargando…
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...
Autores principales: | , , , , |
---|---|
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 |
_version_ | 1784611846526861312 |
---|---|
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. |
format | Online Article Text |
id | pubmed-8654358 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT vanvrankenjonathang assessingtargetengagementusingproteomewidesolventshiftassays AT lijiaming assessingtargetengagementusingproteomewidesolventshiftassays AT mitchelldylanc assessingtargetengagementusingproteomewidesolventshiftassays AT navarretepereajose assessingtargetengagementusingproteomewidesolventshiftassays AT gygistevenp assessingtargetengagementusingproteomewidesolventshiftassays |