High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry–based deubiquitylating enzyme assay for drug discovery
Deubiquitylating enzymes (DUBs) play a vital role in the ubiquitin pathway by editing or removing ubiquitin from their substrate. As breakthroughs within the ubiquitin field continue to highlight the potential of deubiquitylating enzymes as drug targets, there is increasing demand for versatile high...
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| Veröffentlicht in: | Nature protocols 2020-12, Vol.15 (12), p.4034-4057 |
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| creator | De Cesare, Virginia Moran, Jennifer Traynor, Ryan Knebel, Axel Ritorto, Maria Stella Trost, Matthias McLauchlan, Hilary Hastie, C. James Davies, Paul |
| description | Deubiquitylating enzymes (DUBs) play a vital role in the ubiquitin pathway by editing or removing ubiquitin from their substrate. As breakthroughs within the ubiquitin field continue to highlight the potential of deubiquitylating enzymes as drug targets, there is increasing demand for versatile high-throughput (HT) tools for the identification of potent and selective DUB modulators. Here we present the HT adaptation of the previously published MALDI-TOF–based DUB assay method. In a MALDI-TOF DUB assay, we quantitate the amount of mono-ubiquitin generated by the in vitro cleavage of ubiquitin chains by DUBs. The method has been specifically developed for use with nanoliter-dispensing robotics to meet drug discovery requirements for the screening of large and diverse compound libraries. Contrary to the most common DUB screening technologies currently available, the MALDI-TOF DUB assay combines the use of physiological substrates with the sensitivity and reliability of the mass spectrometry–based readout.
The authors describe a protocol for a high-throughput version of the MALDI-TOF–based deubiquitylating enzyme assay method. |
| doi_str_mv | 10.1038/s41596-020-00405-0 |
| format | Article |
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The authors describe a protocol for a high-throughput version of the MALDI-TOF–based deubiquitylating enzyme assay method.</description><identifier>ISSN: 1754-2189</identifier><identifier>EISSN: 1750-2799</identifier><identifier>DOI: 10.1038/s41596-020-00405-0</identifier><identifier>PMID: 33139956</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/154 ; 631/154/556 ; 631/45/474/2289 ; 639/766/930/296 ; Analytical Chemistry ; Assaying ; Biochemical assays ; Biological Techniques ; Biomedical and Life Sciences ; Computational Biology/Bioinformatics ; Drug discovery ; Drug Discovery - methods ; Enzyme Assays - methods ; Enzymes ; Humans ; Ionization ; Ions ; Life Sciences ; Mass spectrometry ; Mass spectroscopy ; Methods ; Microarrays ; Modulators ; Organic Chemistry ; Pharmaceutical research ; Protocol ; Robotics ; Scientific imaging ; Screening ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods ; Spectroscopy ; Substrates ; Therapeutic targets ; Time-of-flight mass spectrometry ; Ubiquitin ; Ubiquitin-proteasome system ; Ubiquitination</subject><ispartof>Nature protocols, 2020-12, Vol.15 (12), p.4034-4057</ispartof><rights>The Author(s), under exclusive licence to Springer Nature Limited 2020</rights><rights>COPYRIGHT 2020 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Dec 2020</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c586t-1b8e2db3a2dea47b7980d885e560567e120d87be56e3a647c8ae601f9f421f3a3</citedby><cites>FETCH-LOGICAL-c586t-1b8e2db3a2dea47b7980d885e560567e120d87be56e3a647c8ae601f9f421f3a3</cites><orcidid>0000-0002-2640-6389 ; 0000-0001-8022-2719 ; 0000-0001-7164-4098</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/s41596-020-00405-0$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/s41596-020-00405-0$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27903,27904,41467,42536,51297</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33139956$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>De Cesare, Virginia</creatorcontrib><creatorcontrib>Moran, Jennifer</creatorcontrib><creatorcontrib>Traynor, Ryan</creatorcontrib><creatorcontrib>Knebel, Axel</creatorcontrib><creatorcontrib>Ritorto, Maria Stella</creatorcontrib><creatorcontrib>Trost, Matthias</creatorcontrib><creatorcontrib>McLauchlan, Hilary</creatorcontrib><creatorcontrib>Hastie, C. James</creatorcontrib><creatorcontrib>Davies, Paul</creatorcontrib><title>High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry–based deubiquitylating enzyme assay for drug discovery</title><title>Nature protocols</title><addtitle>Nat Protoc</addtitle><addtitle>Nat Protoc</addtitle><description>Deubiquitylating enzymes (DUBs) play a vital role in the ubiquitin pathway by editing or removing ubiquitin from their substrate. As breakthroughs within the ubiquitin field continue to highlight the potential of deubiquitylating enzymes as drug targets, there is increasing demand for versatile high-throughput (HT) tools for the identification of potent and selective DUB modulators. Here we present the HT adaptation of the previously published MALDI-TOF–based DUB assay method. In a MALDI-TOF DUB assay, we quantitate the amount of mono-ubiquitin generated by the in vitro cleavage of ubiquitin chains by DUBs. The method has been specifically developed for use with nanoliter-dispensing robotics to meet drug discovery requirements for the screening of large and diverse compound libraries. Contrary to the most common DUB screening technologies currently available, the MALDI-TOF DUB assay combines the use of physiological substrates with the sensitivity and reliability of the mass spectrometry–based readout.
The authors describe a protocol for a high-throughput version of the MALDI-TOF–based deubiquitylating enzyme assay method.</description><subject>631/154</subject><subject>631/154/556</subject><subject>631/45/474/2289</subject><subject>639/766/930/296</subject><subject>Analytical Chemistry</subject><subject>Assaying</subject><subject>Biochemical assays</subject><subject>Biological Techniques</subject><subject>Biomedical and Life Sciences</subject><subject>Computational Biology/Bioinformatics</subject><subject>Drug discovery</subject><subject>Drug Discovery - methods</subject><subject>Enzyme Assays - methods</subject><subject>Enzymes</subject><subject>Humans</subject><subject>Ionization</subject><subject>Ions</subject><subject>Life Sciences</subject><subject>Mass spectrometry</subject><subject>Mass spectroscopy</subject><subject>Methods</subject><subject>Microarrays</subject><subject>Modulators</subject><subject>Organic Chemistry</subject><subject>Pharmaceutical research</subject><subject>Protocol</subject><subject>Robotics</subject><subject>Scientific imaging</subject><subject>Screening</subject><subject>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods</subject><subject>Spectroscopy</subject><subject>Substrates</subject><subject>Therapeutic targets</subject><subject>Time-of-flight mass spectrometry</subject><subject>Ubiquitin</subject><subject>Ubiquitin-proteasome system</subject><subject>Ubiquitination</subject><issn>1754-2189</issn><issn>1750-2799</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9ks1u1DAUhSMEoqXwAixQJDbtwq0dx3ayrAqlIw2qBGVtOclNxlUST20HNV3xDjwBr8aTcKdTqAYhZFn--87xvdJJkteMHjPKi5OQM1FKQjNKKM2pIPRJss-UoCRTZfn0fp-TjBXlXvIihGuEFJfqebLHOeNlKeR-8uPCdisSV95N3Wo9xXQw0dtbYkKwIUKT9iaATxsIzq-jdeMJTntnNts02gGIa0nbo0lMDz-eLt8tyNXl-RHahJCGNdTRuwGin39--16hVYNWU2VvJhvnHl3GLoXxbh4gRYGZ09bhZ37q0saG2n0FP79MnrWmD_DqYT1Ivpy_vzq7IMvLD4uz0yWpRSEjYVUBWVNxkzVgclWpsqBNUQgQkgqpgGV4VBUegRuZq7owIClryzbPWMsNP0gOt75r724mCFEPWAL0vRnBTUFnuVCc0lIKRN_-hV67yY9YHVKKZ3lZFOqR6kwP2o6ti97UG1N9KgUtM8YKidTxPygcDQy2diO0Fu93BEc7AmQi3MbOTCHoxedPu2y2ZWvvQvDQ6rW3g_GzZlRvMqS3GdKYIX2fIU1R9Oahu6kaoPkj-R0aBPgWCPg0duAf2_-P7S_BGtOG</recordid><startdate>20201201</startdate><enddate>20201201</enddate><creator>De Cesare, Virginia</creator><creator>Moran, Jennifer</creator><creator>Traynor, Ryan</creator><creator>Knebel, Axel</creator><creator>Ritorto, Maria Stella</creator><creator>Trost, Matthias</creator><creator>McLauchlan, Hilary</creator><creator>Hastie, C. 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James</au><au>Davies, Paul</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry–based deubiquitylating enzyme assay for drug discovery</atitle><jtitle>Nature protocols</jtitle><stitle>Nat Protoc</stitle><addtitle>Nat Protoc</addtitle><date>2020-12-01</date><risdate>2020</risdate><volume>15</volume><issue>12</issue><spage>4034</spage><epage>4057</epage><pages>4034-4057</pages><issn>1754-2189</issn><eissn>1750-2799</eissn><abstract>Deubiquitylating enzymes (DUBs) play a vital role in the ubiquitin pathway by editing or removing ubiquitin from their substrate. As breakthroughs within the ubiquitin field continue to highlight the potential of deubiquitylating enzymes as drug targets, there is increasing demand for versatile high-throughput (HT) tools for the identification of potent and selective DUB modulators. Here we present the HT adaptation of the previously published MALDI-TOF–based DUB assay method. In a MALDI-TOF DUB assay, we quantitate the amount of mono-ubiquitin generated by the in vitro cleavage of ubiquitin chains by DUBs. The method has been specifically developed for use with nanoliter-dispensing robotics to meet drug discovery requirements for the screening of large and diverse compound libraries. Contrary to the most common DUB screening technologies currently available, the MALDI-TOF DUB assay combines the use of physiological substrates with the sensitivity and reliability of the mass spectrometry–based readout.
The authors describe a protocol for a high-throughput version of the MALDI-TOF–based deubiquitylating enzyme assay method.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>33139956</pmid><doi>10.1038/s41596-020-00405-0</doi><tpages>24</tpages><orcidid>https://orcid.org/0000-0002-2640-6389</orcidid><orcidid>https://orcid.org/0000-0001-8022-2719</orcidid><orcidid>https://orcid.org/0000-0001-7164-4098</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | 631/154 631/154/556 631/45/474/2289 639/766/930/296 Analytical Chemistry Assaying Biochemical assays Biological Techniques Biomedical and Life Sciences Computational Biology/Bioinformatics Drug discovery Drug Discovery - methods Enzyme Assays - methods Enzymes Humans Ionization Ions Life Sciences Mass spectrometry Mass spectroscopy Methods Microarrays Modulators Organic Chemistry Pharmaceutical research Protocol Robotics Scientific imaging Screening Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods Spectroscopy Substrates Therapeutic targets Time-of-flight mass spectrometry Ubiquitin Ubiquitin-proteasome system Ubiquitination |
| title | High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry–based deubiquitylating enzyme assay for drug discovery |
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