Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays
In response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to approximate compound-dependent changes in thermal stability, the proteome-wide thermal shift assa...
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| Format: | Article |
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eLife Sciences Publications Ltd
2024-11-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/95595 |
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| author | Jonathan G Van Vranken Jiaming Li Julian Mintseris Ting-Yu Wei Catherine M Sniezek Meagan Gadzuk-Shea Steven P Gygi Devin K Schweppe |
| author_facet | Jonathan G Van Vranken Jiaming Li Julian Mintseris Ting-Yu Wei Catherine M Sniezek Meagan Gadzuk-Shea Steven P Gygi Devin K Schweppe |
| author_sort | Jonathan G Van Vranken |
| collection | DOAJ |
| description | In response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to approximate compound-dependent changes in thermal stability, the proteome-wide thermal shift assay has emerged as a powerful tool in this arsenal. The most recent iterations have drastically improved the overall efficiency of these assays, providing an opportunity to screen compounds at a previously unprecedented rate. Taking advantage of this advance, we quantified more than one million thermal stability measurements in response to multiple classes of therapeutic and tool compounds (96 compounds in living cells and 70 compounds in lysates). When interrogating the dataset as a whole, approximately 80% of compounds (with quantifiable targets) caused a significant change in the thermal stability of an annotated target. There was also a wealth of evidence portending off-target engagement despite the extensive use of the compounds in the laboratory and/or clinic. Finally, the combined application of cell- and lysate-based assays, aided in the classification of primary (direct ligand binding) and secondary (indirect) changes in thermal stability. Overall, this study highlights the value of these assays in the drug development process by affording an unbiased and reliable assessment of compound mechanism of action. |
| format | Article |
| id | doaj-art-8bf3b9c5353e41d7be11802c16d7f60c |
| institution | OA Journals |
| issn | 2050-084X |
| language | English |
| publishDate | 2024-11-01 |
| publisher | eLife Sciences Publications Ltd |
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| series | eLife |
| spelling | doaj-art-8bf3b9c5353e41d7be11802c16d7f60c2025-08-20T02:13:47ZengeLife Sciences Publications LtdeLife2050-084X2024-11-011310.7554/eLife.95595Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assaysJonathan G Van Vranken0https://orcid.org/0000-0002-8931-852XJiaming Li1Julian Mintseris2Ting-Yu Wei3Catherine M Sniezek4Meagan Gadzuk-Shea5Steven P Gygi6https://orcid.org/0000-0001-7626-0034Devin K Schweppe7https://orcid.org/0000-0002-3241-6276Department of Cell Biology, Harvard Medical School, Boston, United StatesDepartment of Cell Biology, Harvard Medical School, Boston, United StatesDepartment of Cell Biology, Harvard Medical School, Boston, United StatesDepartment of Cell Biology, Harvard Medical School, Boston, United StatesDepartment of Genome Sciences, University of Washington, Seattle, United StatesDepartment of Genome Sciences, University of Washington, Seattle, United StatesDepartment of Cell Biology, Harvard Medical School, Boston, United StatesDepartment of Genome Sciences, University of Washington, Seattle, United StatesIn response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to approximate compound-dependent changes in thermal stability, the proteome-wide thermal shift assay has emerged as a powerful tool in this arsenal. The most recent iterations have drastically improved the overall efficiency of these assays, providing an opportunity to screen compounds at a previously unprecedented rate. Taking advantage of this advance, we quantified more than one million thermal stability measurements in response to multiple classes of therapeutic and tool compounds (96 compounds in living cells and 70 compounds in lysates). When interrogating the dataset as a whole, approximately 80% of compounds (with quantifiable targets) caused a significant change in the thermal stability of an annotated target. There was also a wealth of evidence portending off-target engagement despite the extensive use of the compounds in the laboratory and/or clinic. Finally, the combined application of cell- and lysate-based assays, aided in the classification of primary (direct ligand binding) and secondary (indirect) changes in thermal stability. Overall, this study highlights the value of these assays in the drug development process by affording an unbiased and reliable assessment of compound mechanism of action.https://elifesciences.org/articles/95595proteomicsthermal proteome profilinghuman cell lineschemoproteomicskinase inhibitors |
| spellingShingle | Jonathan G Van Vranken Jiaming Li Julian Mintseris Ting-Yu Wei Catherine M Sniezek Meagan Gadzuk-Shea Steven P Gygi Devin K Schweppe Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays eLife proteomics thermal proteome profiling human cell lines chemoproteomics kinase inhibitors |
| title | Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays |
| title_full | Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays |
| title_fullStr | Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays |
| title_full_unstemmed | Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays |
| title_short | Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays |
| title_sort | large scale characterization of drug mechanism of action using proteome wide thermal shift assays |
| topic | proteomics thermal proteome profiling human cell lines chemoproteomics kinase inhibitors |
| url | https://elifesciences.org/articles/95595 |
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