Chemical proteomics: ligation and cleavage of protein modifications

Rudolf, Georg C.; Heydenreuter, Wolfgang; Sieber, Stephan A.

doi:10.1016/j.cbpa.2012.11.007

Cited by 49 publications

(39 citation statements)

References 45 publications

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“…On the other hand, it is the usage of formic acid that makes our current approach not applicable to compounds that are acid-labile. For these compounds, a potential solution is to change our current acid-cleavable linker to other types of linkers2122232429.…”

Section: Discussionmentioning

confidence: 99%

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Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)

Wang

Zhang

et al. 2015

Sci Rep

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Target-identification and understanding of mechanism-of-action (MOA) are challenging for development of small-molecule probes and their application in biology and drug discovery. For example, although aspirin has been widely used for more than 100 years, its molecular targets have not been fully characterized. To cope with this challenge, we developed a novel technique called quantitative acid-cleavable activity-based protein profiling (QA-ABPP) with combination of the following two parts: (i) activity-based protein profiling (ABPP) and iTRAQ™ quantitative proteomics for identification of target proteins and (ii) acid-cleavable linker-based ABPP for identification of peptides with specific binding sites. It is known that reaction of aspirin with its target proteins leads to acetylation. We thus applied the above technique using aspirin-based probes in human cancer HCT116 cells. We identified 1110 target proteins and 2775 peptides with exact acetylation sites. By correlating these two sets of data, 523 proteins were identified as targets of aspirin. We used various biological assays to validate the effects of aspirin on inhibition of protein synthesis and induction of autophagy which were elicited from the pathway analysis of Aspirin target profile. This technique is widely applicable for target identification in the field of drug discovery and biology, especially for the covalent drugs.

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Section: Discussionmentioning

confidence: 99%

“…The quantitative information generated from such approaches can help differentiate specific from non-specific bindings by comparing enrichment ratios. Meanwhile, a variety of cleavable linkers have been developed and used in ABPP21222324. Cleavable linkers allow the seized proteins to be liberated after pull down under non-denaturing conditions.…”

mentioning

confidence: 99%

Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)

Wang

Zhang

et al. 2015

Sci Rep

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“…[1] These reactions include the Staudinger ligation, the azide-cyclooctyne cycloaddition, and the inverse-electron-demand Diels-Alder (inv-DA) reaction. [3] Although these linkers are selective, they often lack the level of bioorthogonality and broad applicability of the click reactions, which is especially relevant when extending the application scope to living cells, animals, and humans. [3] Although these linkers are selective, they often lack the level of bioorthogonality and broad applicability of the click reactions, which is especially relevant when extending the application scope to living cells, animals, and humans.…”

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confidence: 99%

Click to Release: Instantaneous Doxorubicin Elimination upon Tetrazine Ligation

et al. 2013

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Die schnellste Klick‐Reaktion, die hoch selektive Diels‐Alder‐Reaktion mit inversem Elektronenbedarf, wurde so modifiziert, dass sie selektive bioorthogonale Freisetzungen ermöglicht. Auf diese Weise führte die Reaktion eines Tetrazins mit einem wirkstoffgebundenen trans‐Cycloocten zur augenblicklichen Freisetzung des Wirkstoffs und von CO2 (siehe Schema). Eine mögliche Anwendung ist die chemisch ausgelöste Freisetzung und Aktivierung eines Wirkstoffs aus einem tumorgebundenen Antikörper‐Wirkstoff‐Konjugat.

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“…[7][8][9][10][11][12] Chemical cross-linking of gelatin can, for example, be achieved by radical cross-linking of methacryl-modified gelatin (GM). de Another possibility is the immobilization of proteins through photocleavable linkers [29] which was already applied for proteomics, [36,37] was further used to control protein adsorption to surfaces [38][39][40][41][42][43] and has since gained certain interest in the field of controlled release of small molecule drugs or model therapeutics [44][45][46][47][48][49][50] as well. de Another possibility is the immobilization of proteins through photocleavable linkers [29] which was already applied for proteomics, [36,37] was further used to control protein adsorption to surfaces [38][39][40][41][42][43] and has since gained certain interest in the field of controlled release of small molecule drugs or model therapeutics [44][45][46][47][48][49][50] as well.…”

Section: Introductionmentioning

confidence: 99%

Photoinduced Cleavage and Hydrolysis of o‐Nitrobenzyl Linker and Covalent Linker Immobilization in Gelatin Methacryloyl Hydrogels

Claaßen

Gohl

et al. 2018

Macromolecular Bioscience

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Light-induced release systems can be triggered remotely and are of interest for many controlled release applications due to the possibility for spatio-temporal release control. In this study a biotin-functionalized photocleavable macromer is incorporated with an o-nitrobenzyl moiety into gelatin methacryloyl(-acetyl) hydrogels via radical cross-linking. Stronger immobilization of streptavidin-coupled horseradish peroxidase occurs in linker-functionalized hydrogels compared to pure gelatin methacryloyl(-acetyl) hydrogels, and a controlled release of the streptavidin conjugate upon UV-irradiation is possible. Liquid chromatography coupled to mass spectrometry (LC-MS) analysis of aqueous linker solutions allows the identification of the main cleavage products and the cleavage kinetics. Thus, it is shown that a significant hydrolysis of the linker occurs at 37 °C. Nevertheless the system reported here is a promising controlled release scaffold for proteins and application in tissue engineering, if background releases of the immobilized drug are tolerable.

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Chemical proteomics: ligation and cleavage of protein modifications

Cited by 49 publications

References 45 publications

Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)

Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)

Click to Release: Instantaneous Doxorubicin Elimination upon Tetrazine Ligation

Photoinduced Cleavage and Hydrolysis of o‐Nitrobenzyl Linker and Covalent Linker Immobilization in Gelatin Methacryloyl Hydrogels

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