WO2016201257A3 - Compositions and methods for identifying adp-ribosylated sites by mass spectrometry - Google Patents

Compositions and methods for identifying adp-ribosylated sites by mass spectrometry Download PDF

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Publication number
WO2016201257A3
WO2016201257A3 PCT/US2016/036934 US2016036934W WO2016201257A3 WO 2016201257 A3 WO2016201257 A3 WO 2016201257A3 US 2016036934 W US2016036934 W US 2016036934W WO 2016201257 A3 WO2016201257 A3 WO 2016201257A3
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WO
WIPO (PCT)
Prior art keywords
mass spectrometry
adp
identifying
methods
ribosylated
Prior art date
Application number
PCT/US2016/036934
Other languages
French (fr)
Other versions
WO2016201257A2 (en
Inventor
Anthony K. LEUNG
Sandra B. GABELLI
Casey M. DANIELS
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The Johns Hopkins University
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Publication date
Application filed by The Johns Hopkins University filed Critical The Johns Hopkins University
Publication of WO2016201257A2 publication Critical patent/WO2016201257A2/en
Publication of WO2016201257A3 publication Critical patent/WO2016201257A3/en

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12PFERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P21/00Preparation of peptides or proteins
    • C12P21/005Glycopeptides, glycoproteins
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/34Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/34Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase
    • C12Q1/37Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase involving peptidase or proteinase
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12YENZYMES
    • C12Y304/00Hydrolases acting on peptide bonds, i.e. peptidases (3.4)
    • C12Y304/21Serine endopeptidases (3.4.21)
    • C12Y304/21004Trypsin (3.4.21.4)
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12YENZYMES
    • C12Y306/00Hydrolases acting on acid anhydrides (3.6)
    • C12Y306/01Hydrolases acting on acid anhydrides (3.6) in phosphorus-containing anhydrides (3.6.1)
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6848Methods of protein analysis involving mass spectrometry
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00Detection or diagnosis of diseases
    • G01N2800/70Mechanisms involved in disease identification
    • G01N2800/7033Non-proliferative mechanisms

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • General Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Physics & Mathematics (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Immunology (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Biomedical Technology (AREA)
  • Hematology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Urology & Nephrology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Cell Biology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Other Investigation Or Analysis Of Materials By Electrical Means (AREA)
  • Enzymes And Modification Thereof (AREA)

Abstract

The present disclosure relates to the use of a nudix hydrolase(RppH or NudT16) to cleave poly ADP-ribosylated proteins and leave a tag (phosphoribose) to be analyzed by mass spectrometry to identify post-translational modification (PTM) profiles of proteins. The disclosure relates to methods for identifying an ADP- ribosylation profile in hydrolyzed proteins using mass spectrometry.
PCT/US2016/036934 2015-06-10 2016-06-10 Compositions and methods for identifying adp-ribosylated sites by mass spectrometry WO2016201257A2 (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US201562173554P 2015-06-10 2015-06-10
US62/173,554 2015-06-10
US201562264834P 2015-12-08 2015-12-08
US62/264,834 2015-12-08

Publications (2)

Publication Number Publication Date
WO2016201257A2 WO2016201257A2 (en) 2016-12-15
WO2016201257A3 true WO2016201257A3 (en) 2017-02-23

Family

ID=57504036

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2016/036934 WO2016201257A2 (en) 2015-06-10 2016-06-10 Compositions and methods for identifying adp-ribosylated sites by mass spectrometry

Country Status (1)

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WO (1) WO2016201257A2 (en)

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015073818A1 (en) * 2013-11-14 2015-05-21 The Brigham And Women's Hospital, Inc. Parp9 and parp14 as key regulators of macrophage activation
US10221191B2 (en) 2015-12-22 2019-03-05 SHY Therapeutics LLC Compounds for the treatment of cancer and inflammatory disease
KR102736865B1 (en) 2017-06-21 2024-12-03 샤이 테라퓨틱스 엘엘씨 Compounds that interact with the Ras superfamily for the treatment of cancer, inflammatory diseases, neurodevelopmental diseases and fibrotic diseases
GB201810697D0 (en) * 2018-06-29 2018-08-15 Imperial Innovations Ltd ADP-ribosylation profiling
US12391705B2 (en) 2018-12-19 2025-08-19 Shy Therapeutics, Llc Compounds that interact with the Ras superfamily for the treatment of cancers, inflammatory diseases, rasopathies, and fibrotic disease
CN110590769B (en) * 2019-06-13 2021-09-24 中山大学 A pair of quinazolinone alkaloid enantiomers and their preparation method and application
AU2021217816A1 (en) * 2020-02-03 2022-08-11 Gt Gain Therapeutics Sa Combination therapy for treating MPS1
US20230158028A1 (en) * 2020-04-06 2023-05-25 The Regents Of The University Of California Compounds and methods for inducing ucp1 expression
TW202214574A (en) * 2020-06-08 2022-04-16 加拿大商愛彼特生物製藥公司 Substituted (phthalazin-1-ylmethyl)ureas, substituted n-(phthalazin-1-ylmethyl)amides, and analogues thereof
WO2024141660A2 (en) * 2022-12-30 2024-07-04 Aexon Labs. Inc. Dihydro-quinazoline, -benzothiazine and -benzoxazine derivatives and use thereof as orexin receptors agonists for treating or preventing neurological diseases

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090155834A1 (en) * 1999-12-15 2009-06-18 Massachusetts Institute Of Technology Methods for identifying agents which alter histone protein acetylation, decrease aging or increase lifespan
WO2009077521A1 (en) * 2007-12-17 2009-06-25 Fondazione Telethon Method for the isolation and identification of adp-ribosylated molecules
US20100069372A1 (en) * 2005-11-07 2010-03-18 The General Hospital Corporation Compositions and methods for modulating poly(adp-ribose) polymerase activity
US20130252999A1 (en) * 2006-12-07 2013-09-26 China Medical University 2-phenyl-4-quinolones as anticancer agents

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090155834A1 (en) * 1999-12-15 2009-06-18 Massachusetts Institute Of Technology Methods for identifying agents which alter histone protein acetylation, decrease aging or increase lifespan
US20100069372A1 (en) * 2005-11-07 2010-03-18 The General Hospital Corporation Compositions and methods for modulating poly(adp-ribose) polymerase activity
US20130252999A1 (en) * 2006-12-07 2013-09-26 China Medical University 2-phenyl-4-quinolones as anticancer agents
WO2009077521A1 (en) * 2007-12-17 2009-06-25 Fondazione Telethon Method for the isolation and identification of adp-ribosylated molecules

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
DANIELS ET AL.: "Nudix hydrolases degrade proteinconjugated ADP-ribose", SCIENTIFIC REPORTS, vol. 5, 16 December 2015 (2015-12-16), pages 1 - 12, XP055364610 *
DOLLE ET AL.: "NAD and ADP-ribose metabolism in mitochondria", FEBS JOURNAL, vol. 280, no. 15, 3 June 2013 (2013-06-03), pages 3530 - 3541, XP055364613 *
PALAZZO ET AL.: "Processing of protein ADP-ribosylation by Nudix hydrolases", BIOCHEM J., vol. 468, no. 2, 19 March 2015 (2015-03-19), pages 293 - 301, XP055364465 *
WAHLBERG ET AL.: "Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors", NATURE BIOTECHNOLOGY, vol. 30, no. 3, 19 February 2012 (2012-02-19), pages 283 - 288, XP008163087 *

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Publication number Publication date
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