Epigenetic drug target deconvolution by mass spectrometry–based technologies

Bioorthogonal chemistry is a mainstay of chemoproteomic sample preparation workflows. While numerous transformations are now available, chemoproteomic studies still rely overwhelmingly on copper-catalyzed azide –alkyne cycloaddition (CuAAC) or 'click' chemistry. Here we demonstrate that gel-based activity-based protein profiling (ABPP) and mass-spectrometry-based chemoproteomic profiling can be conducted using Suzuki–Miyaura cross-coupling. We identify reaction conditions that proceed in complex cell lysates and find that Suzuki –Miyaura cross-coupling and CuAAC yield comparable chemoproteomic coverage. Importantly, Suzuki–Miyaura is also compatible with chemoproteomic target deconvolution, as demonstrated using structurally matched probes tailored to react with the cysteine protease caspase-8. Uniquely enabled by the observed orthogonality of palladium-catalyzed cross-coupling and CuAAC, we combine both reactions to achieve dual protein labeling.

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Integration of Mass Spectrometry Imaging and Machine Learning Visualizes Region-Specific Age-Induced and Drug-Target Metabolic Perturbations in the Brain

ACS Chemical Neuroscience ◽

10.1021/acschemneuro.1c00103 ◽

2021 ◽

Author(s):

Theodosia Vallianatou ◽

Reza Shariatgorji ◽

Anna Nilsson ◽

Maria Karlgren ◽

Heather Hulme ◽

...

Keyword(s):

Machine Learning ◽

Mass Spectrometry ◽

Drug Target ◽

Mass Spectrometry Imaging ◽

The Brain

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Drug Target Identification in Tissues by Thermal Proteome Profiling

The Annual Review of Pharmacology and Toxicology ◽

10.1146/annurev-pharmtox-052120-013205 ◽

2021 ◽

Vol 62 (1) ◽

Author(s):

André Mateus ◽

Nils Kurzawa ◽

Jessica Perrin ◽

Giovanna Bergamini ◽

Mikhail M. Savitski

Keyword(s):

Drug Target ◽

Target Identification ◽

Annual Review ◽

Publication Date ◽

Proteome Profiling ◽

Biological Phenomena ◽

Target Deconvolution ◽

Drug Target Identification ◽

Recent Developments ◽

Fundamental Biology

Drug target deconvolution can accelerate the drug discovery process by identifying a drug's targets (facilitating medicinal chemistry efforts) and off-targets (anticipating toxicity effects or adverse drug reactions). Multiple mass spectrometry–based approaches have been developed for this purpose, but thermal proteome profiling (TPP) remains to date the only one that does not require compound modification and can be used to identify intracellular targets in living cells. TPP is based on the principle that the thermal stability of a protein can be affected by its interactions. Recent developments of this approach have expanded its applications beyond drugs and cell cultures to studying protein-drug interactions and biological phenomena in tissues. These developments open up the possibility of studying drug treatment or mechanisms of disease in a holistic fashion, which can result in the design of better drugs and lead to a better understanding of fundamental biology. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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