Catalytic activation of pre-substrates via dynamic Fragment assembly on Protein templates
Creators: name: Burda, E.
name: Rademann, Jörg
Publisher: name: Freie Universität Berlin
Year: 2014
Subjects: subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie

description: Sensitive detection of small molecule fragments binding to defined sites of biomacromolecules is still a considerable challenge. Here we demonstrate that protein-binding fragments are able to induce enzymatic reactions on the protein surface via dynamic fragment ligation. Fragments binding to the S1 pocket of serine proteases containing a nitrogen, oxygen or sulphur nucleophile are found to activate electrophilic pre-substrates through a reversible, covalent ligation reaction. The dynamic ligation reaction positions the pre-substrate molecule at the active site of the protein thereby inducing its enzymatic cleavage. Catalytic activation of pre-substrates is confirmed by fluorescence spectroscopy and by high-performance liquid chromatography. The approach is investigated with 3 pre-substrates and 14 protein-binding fragments and the specific activation and the templating effect exerted by the enzyme is quantified for each protease–fragment–pre- substrate combination. The described approach enables the site-specific identification of protein-binding fragments, the functional characterization of enzymatic sites and the quantitative analysis of protein template-assisted ligation reactions. View full text Subject terms: Chemical sciences Chemical biology Medicinal chemistry At a glance Figures First | 1-4 of 6 | Last View all figures left The concept of pre-substrate activation by protein-binding fragments. Figure 1 Proof-of-concept. Figure 2 Structure of potential pre- substrates 1–3 and S1-binding fragments 4–17. Figure 3 Model for the activation of pre-substrates by nucleophilic protein-binding fragments. Figure 4 Activation of pre-substrate 3. Figure 5 Three-fragment assembly. Figure 6 right Compounds Genes and Proteins References Abstract• References• Author information• Supplementary information Rees, D. C., Congreve, M., Murray, C. W. &amp; Carr, R. Fragment-based lead discovery. Nat. Rev. Drug Discov. 3, 660–672 (2004). 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E. &amp; Bowman, C. N. Thiol-ene click chemistry. Angew. Chem. Int. Ed. 49, 1540–1573 (2010). CAS ISI Article Download references Author information Abstract• References• Author information• Supplementary information Affiliations Institute of Pharmacy, Medicinal Chemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany Edyta Burda &amp; Jörg Rademann Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Straße 2+4, 14195 Berlin, Germany Jörg Rademann Contributions J.R. and E.B. conceived and designed the experiments, E.B. performed the experiments. Both authors discussed the results and co-wrote the manuscript. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: Jörg Rademann Supplementary information Abstract• References• Author information• Supplementary information PDF files Supplementary Information (915 KB) Supplementary Figures 1-11, Supplementary Methods and Supplementary References. 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Oftentim… Wireless Internet Connectivity for Field Applications Deadline: Apr 05 2015 Reward: $20,000 USD Data collection in outdoor field studies is problematic and inefficient without a reliable wireless internet connection. The… Powered by:innocentive Sensitive detection of small molecule fragments binding to defined sites of biomacromolecules is still a considerable challenge. Here we demonstrate that protein-binding fragments are able to induce enzymatic reactions on the protein surface via dynamic fragment ligation. Fragments binding to the S1 pocket of serine proteases containing a nitrogen, oxygen or sulphur nucleophile are found to activate electrophilic pre-substrates through a reversible, covalent ligation reaction. The dynamic ligation reaction positions the pre-substrate molecule at the active site of the protein thereby inducing its enzymatic cleavage. Catalytic activation of pre-substrates is confirmed by fluorescence spectroscopy and by high-performance liquid chromatography. The approach is investigated with 3 pre-substrates and 14 protein-binding fragments and the specific activation and the templating effect exerted by the enzyme is quantified for each protease–fragment–pre- substrate combination. The described approach enables the site-specific identification of protein-binding fragments, the functional characterization of enzymatic sites and the quantitative analysis of protein template-assisted ligation reactions.