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      Funktionalisierte Cofaktor‐Analoga für die Erforschung von Interaktomen und darüber hinaus

      1 , 1 , 1
      Angewandte Chemie
      Wiley

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          Abstract

          Cofaktoren werden für beinahe die Hälfte aller Enzymreaktionen benötigt. Ihre Funktionen und Bindungspartner sind jedoch auch nach jahrzehntelanger Forschung noch nicht vollständig verstanden. Funktionalisierte Cofaktoren (Analoga), die anstelle des natürlichen Cofaktors binden, können darauf Antworten liefern und den Aktivitätsbereich des jeweiligen Cofaktors aufklären. Mithilfe chemischer Proteomik‐Ansätze wie des aktivitätsbasierten Protein‐Profilings können das Interaktom und die Lokalisierung des nativen Cofaktors in seiner physiologischen Umgebung entschlüsselt und bisher uncharakterisierte Proteine annotiert werden. Darüber hinaus können Cofaktoren, die funktionelle Gruppen an Substrat‐Biomoleküle übertragen, genutzt werden, um als Analoge Enzyme ortsspezifisch zu markieren und die komplexe Biologie der posttranslationalen Proteinmodifikation zu untersuchen. Die vielfältige Aktivität von Cofaktoren hat die Entwicklung von deren Analoga für den Einsatz als Inhibitoren, Antibiotika sowie Chemo‐ und Biosensoren inspiriert. Darüber hinaus haben Cofaktor‐Konjugate die Herstellung neuartiger Enzyme und künstlicher DNA‐Enzyme ermöglicht.

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          Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry.

          The direct detection of drug-protein interactions in living cells is a major challenge in drug discovery research. Recently, we introduced an approach termed thermal proteome profiling (TPP), which enables the monitoring of changes in protein thermal stability across the proteome using quantitative mass spectrometry. We determined the intracellular thermal profiles for up to 7,000 proteins, and by comparing profiles derived from cultured mammalian cells in the presence or absence of a drug we showed that it was possible to identify direct and indirect targets of drugs in living cells in an unbiased manner. Here we demonstrate the complete workflow using the histone deacetylase inhibitor panobinostat. The key to this approach is the use of isobaric tandem mass tag 10-plex (TMT10) reagents to label digested protein samples corresponding to each temperature point in the melting curve so that the samples can be analyzed by multiplexed quantitative mass spectrometry. Important steps in the bioinformatic analysis include data normalization, melting curve fitting and statistical significance determination of compound concentration-dependent changes in protein stability. All analysis tools are made freely available as R and Python packages. The workflow can be completed in 2 weeks.
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            Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors.

            We describe a chemical proteomics approach to profile the interaction of small molecules with hundreds of endogenously expressed protein kinases and purine-binding proteins. This subproteome is captured by immobilized nonselective kinase inhibitors (kinobeads), and the bound proteins are quantified in parallel by mass spectrometry using isobaric tags for relative and absolute quantification (iTRAQ). By measuring the competition with the affinity matrix, we assess the binding of drugs to their targets in cell lysates and in cells. By mapping drug-induced changes in the phosphorylation state of the captured proteome, we also analyze signaling pathways downstream of target kinases. Quantitative profiling of the drugs imatinib (Gleevec), dasatinib (Sprycel) and bosutinib in K562 cells confirms known targets including ABL and SRC family kinases and identifies the receptor tyrosine kinase DDR1 and the oxidoreductase NQO2 as novel targets of imatinib. The data suggest that our approach is a valuable tool for drug discovery.
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              A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication

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                Author and article information

                Contributors
                (View ORCID Profile)
                (View ORCID Profile)
                Journal
                Angewandte Chemie
                Angewandte Chemie
                Wiley
                0044-8249
                1521-3757
                July 18 2022
                May 31 2022
                July 18 2022
                : 134
                : 29
                Affiliations
                [1 ] Centre for Functional Protein Assemblies Technische Universität München Ernst-Otto-Fischer-Straße 8 85748 Garching Deutschland
                Article
                10.1002/ange.202201136
                ebc5d11d-719c-4bbc-818a-7551b9077e41
                © 2022

                http://creativecommons.org/licenses/by-nc/4.0/

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