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Profiling the Protein Targets of Unmodified Bio-Active Molecules with Drug Affinity Responsive Target Stability and Liquid Chromatography/Tandem Mass Spectrometry

Hwang, Hui Yun ; Kim, Tae Young ; Szász, Marcell A. LU ; Dome, Balazs LU ; Malm, Johan LU ; Marko-Varga, Gyorgy LU and Kwon, Ho Jeong LU (2020) In Proteomics 20(9).
Abstract

Identifying the target proteins of bioactive small molecules is a key step in understanding mode-of-action of the drug and addressing the underlying mechanisms responsible for a particular phenotype. Proteomics has been successfully used to elucidate the target protein profiles of unmodified and ligand-modified bioactive small molecules. In the latter approach, compounds can be modified via click chemistry and combined with activity-based protein profiling. Target proteins are then enriched by performing a pull-down with the modified ligand. Methods that utilize unmodified bioactive small molecules include the cellular thermal shift assay, thermal proteome profiling, stability of proteins from rates of oxidation, and the drug affinity... (More)

Identifying the target proteins of bioactive small molecules is a key step in understanding mode-of-action of the drug and addressing the underlying mechanisms responsible for a particular phenotype. Proteomics has been successfully used to elucidate the target protein profiles of unmodified and ligand-modified bioactive small molecules. In the latter approach, compounds can be modified via click chemistry and combined with activity-based protein profiling. Target proteins are then enriched by performing a pull-down with the modified ligand. Methods that utilize unmodified bioactive small molecules include the cellular thermal shift assay, thermal proteome profiling, stability of proteins from rates of oxidation, and the drug affinity responsive target stability (DARTS) determination (or read-out). This review highlights recent proteomic approaches utilizing data-dependent analysis and data-independent analysis to identify target proteins by DARTS. When combined with liquid chromatography/tandem mass spectrometry, DARTS enables the identification of proteins that bind to drug molecules that leads to a conformational change in the target protein(s). In addition, an effective strategy is proposed for selecting the target protein(s) from within the pool of analyzed candidates. With additional complementary methods, the biologically relevant target proteins that bind to the small bio-active molecules can be further validated.

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author
; ; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
drug affinity responsive stability and liquid chromatography/mass spectrometry, protein identification, sequential window acquisition of all theoretical spectra, target validation
in
Proteomics
volume
20
issue
9
article number
1900325
publisher
John Wiley & Sons Inc.
external identifiers
  • scopus:85079054773
  • pmid:31926115
ISSN
1615-9853
DOI
10.1002/pmic.201900325
language
English
LU publication?
yes
id
c6ebcd96-d7a7-465a-aebd-83e9d08f4e26
date added to LUP
2020-02-17 14:01:26
date last changed
2024-04-03 01:55:54
@article{c6ebcd96-d7a7-465a-aebd-83e9d08f4e26,
  abstract     = {{<p>Identifying the target proteins of bioactive small molecules is a key step in understanding mode-of-action of the drug and addressing the underlying mechanisms responsible for a particular phenotype. Proteomics has been successfully used to elucidate the target protein profiles of unmodified and ligand-modified bioactive small molecules. In the latter approach, compounds can be modified via click chemistry and combined with activity-based protein profiling. Target proteins are then enriched by performing a pull-down with the modified ligand. Methods that utilize unmodified bioactive small molecules include the cellular thermal shift assay, thermal proteome profiling, stability of proteins from rates of oxidation, and the drug affinity responsive target stability (DARTS) determination (or read-out). This review highlights recent proteomic approaches utilizing data-dependent analysis and data-independent analysis to identify target proteins by DARTS. When combined with liquid chromatography/tandem mass spectrometry, DARTS enables the identification of proteins that bind to drug molecules that leads to a conformational change in the target protein(s). In addition, an effective strategy is proposed for selecting the target protein(s) from within the pool of analyzed candidates. With additional complementary methods, the biologically relevant target proteins that bind to the small bio-active molecules can be further validated.</p>}},
  author       = {{Hwang, Hui Yun and Kim, Tae Young and Szász, Marcell A. and Dome, Balazs and Malm, Johan and Marko-Varga, Gyorgy and Kwon, Ho Jeong}},
  issn         = {{1615-9853}},
  keywords     = {{drug affinity responsive stability and liquid chromatography/mass spectrometry; protein identification; sequential window acquisition of all theoretical spectra; target validation}},
  language     = {{eng}},
  number       = {{9}},
  publisher    = {{John Wiley & Sons Inc.}},
  series       = {{Proteomics}},
  title        = {{Profiling the Protein Targets of Unmodified Bio-Active Molecules with Drug Affinity Responsive Target Stability and Liquid Chromatography/Tandem Mass Spectrometry}},
  url          = {{http://dx.doi.org/10.1002/pmic.201900325}},
  doi          = {{10.1002/pmic.201900325}},
  volume       = {{20}},
  year         = {{2020}},
}