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. & Carr, R. Fragment-based lead discovery. Nat. Rev. Drug Discov. 3, 660–672 (2004). CAS ISI PubMed Article Hajduk, P. J. & Greer, J. A decade of fragment- based drug design: strategic advances and lessons learned. Nat. Rev. Drug Discov. 6, 211–219 (2007). CAS ISI PubMed Article Erlanson, D. A., McDowell, R. S. & O’Brien, T. Fragment-based drug discovery. J. Med. Chem. 47, 3463–3482 (2004). CAS ISI PubMed Article Fattori, D., Squarcia, A. & Bartoli, S. Fragment-based approach to drug lead discovery. Drugs RD 9, 217–227 (2008). ISI Article Rademann, J. Organic protein chemistry: drug discovery through the chemical modification of proteins. Angew. Chem. Int. Ed. 43, 4554–4556 (2004). Article Corbett, P. T. et al. Dynamic combinatorial chemistry. Chem. Rev. 106, 3652–3711 (2006). CAS ISI PubMed Article Erlanson, D. A. Fragment-based lead discovery: a chemical update. Curr. Opin. Biotechnol. 17, 643–652 (2006). CAS ISI PubMed Article Schmidt, M. F. & Rademann, J. Dynamic template-assisted strategies in fragment-based drug discovery. Trends Biotechnol. 27, 512–521 (2009). CAS ISI PubMed Article Shuker, S. B., Hajduk, P. J., Meadows, R. P. & Fesik, S. W. Discovering high-affinity ligands for proteins: SAR by NMR. Science 274, 1531–1534 (1996). CAS ISI PubMed Article Vongvilai, P., Angelin, M., Larsson, R. & Ramström, O. Dynamic combinatorial resolution: direct asymmetric lipase-mediated screening of dynamic nitroaldol library. Angew. Chem. Int. Ed. 46, 948–950 (2007). CAS Article Nienaber, V. L. et al. Discovering novel ligands for macromolecules using X-ray crystallographic screening. Nat. Biotechnol. 18, 1105–1108 (2000). CAS ISI PubMed Article Blundell, T. L., Jhoti, H. & Abell, C. High-throughput crystallography for lead discovery in drug design. Nat. Rev. Drug Discov. 1, 45–54 (2002). CAS ISI PubMed Article Sharff, A. & Jhoti, H. High-throughput crystallographyto enhance drug discovery. Curr. Opin. Chem. Biol. 7, 340–345 (2003). CAS ISI PubMed Article Sanders, W. J. et al. Discovery of potent inhibitors of dihydroneopterin aldolase using CrystaLEAD high-throughput X-ray crystallographic screening and structure-directed lead optimization. J. Med. Chem. 47, 1709–1718 (2004). CAS ISI PubMed Article Patterson, A. W., Wood, W. J. L. & Ellman, J. A. Substrate activity screening (SAS): a general procedure for the preparation and screening of a fragment-based non-peptidic protease substrate library for inhibitor discovery. Nat. Protoc. 2, 424–433 (2007). ISI PubMed Article Mares-Guia, M. & Shaw, E. Substrate side chain guanidines as model of the binding of amidines and studies on the active center of trypsin. J. Biol. Chem. 240, 1579–1585 (1965). CAS PubMed Schmidt, M. F. et al. Sensitized detection of inhibitory fragments and iterative development of non- peptidic protease inhibitors by dynamic ligation screening. Angew. Chem. Int. Ed. 47, 3275–3278 (2008). Article Schmidt, M. F., El-Dahshan, A., Keller, S. & Rademann, J. Selective identification of cooperatively binding fragments in a high-throughput ligation assay enables development of a picomolar caspase-3 inhibitor. Angew. Chem. Int. Ed. 48, 6346–6349 (2009). CAS Article Schmidt, M. F., Groves, M. & Rademann, J. Dynamic substrate enhancement for the identification of specific, second-site-binding fragments targeting a set of protein tyrosine phosphatases. Chembiochem 12, 2640–2646 (2011). ISI PubMed Article Al-Gharabli, S. I. et al. An efficient method for the synthesis of peptide aldehyde libraries employed in the discovery of reversible SARS coronavirus main protease (SARS-CoV Mpro) inhibitors. Chembiochem 7, 1048–1055 (2006). ISI PubMed Article Reek J. N. H., Otto S. (eds)Dynamic Combinatorial Chemistry Wiley-VCH (2010). Osowska, K. & Miljanic, O. S. Oxidative kinetic self-sorting of a dynamic imine library. J. Am. Chem. Soc. 133, 724–727 (2011). ISI PubMed Article Hermann, A. Dynamic mixtures and combinatorial libraries: imines as probes for molecular evolution at the interface between chemistry and biology. Org. Biomol. Chem. 7, 3195–3204 (2009). PubMed Article Meyer, C. D., Joiner, C. S. & Stoddart, J. F. Template-directed synthesis employing reversible imine bond formation. Chem. Soc. Rev. 36, 1705–1723 (2007). CAS ISI PubMed Article Rodriguez-Decampo, Z. & Otto, S. Orthogonal or simultaneous use of disulfide and hydrazone exchange in dynamic covalent chemistry in aqueous solution. Chem. Commun. 5301–5303 (2008). Dirksen, A., Yegneswaran, S. & Dawson, P. E. Bisaryl hydrazones as exchangeable biocompatible linkers. Angew. Chem. Int. Ed. 49, 2023–2027 (2010). CAS Article Soutullo, M. D., O’Brien, R. A., Gaines, K. E. & Davis, J. H. Jr Constitutional dynamic systems of ionic and molecular liquids. Chem. Commun. 2529–2531 (2009). Drahonovsky, D. & Lehn, J.-M. Hemiacetals in dynamic covalent chemistry: formation, exchange, selection and modulation processes. J. Org. Chem. 74, 8428–8432 (2009). ISI PubMed Article Caraballo, R., Dong, H., Ribeiro, J. P., Jimenez-Barbero, J. & Ramström, O. Direct STD NMR identification of β-galactosidase inhibitors from a virtual dynamic hemithioacetal system. Angew. Chem. Int. Ed. 49, 589–593 (2010). Article Cacciapaglia, R., Di Stefano, S. & Mandolini, L. Metathesis reaction of formaldehyde acetals: an easy entry into the dynamic covalent chemistry of cyclophane formation. J. Am. Chem. Soc. 127, 13666–13671 (2005). ISI PubMed Article Berkovich-Berger, D. & Lemcoff, N. G. Facile acetal dynamic combinatorial library. Chem. Commun. 1686–1688 (2008). Larsson, R., Pei, Z. & Ramström, O. Catalytic self-screening of cholinesterase substrates from a dynamic combinatorial thioester library. Angew. Chem. Int. Ed. 43, 3716–3718 (2004). Article Shi, B. & Greaney, M. F. Reversible Michael addition of thiols as a new tool for dynamic combinatorial chemistry. Chem. Commun. 886–888 (2005). de Candia, M., Lopopolo, G. & Altomare, C. Novel factor Xa inhibitors: a patent review. Expert Opin. Ther. Pat. 19, 1535–1580 (2009). PubMed Article Schröder Leiros, H.-H. et al. Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements. Protein Sci. 13, 1056–1070 (2004). PubMed Article List, B., Lerner, R. A. & Barbas, C. F. III Proline-catalyzed direct asymmetric aldol reactions. J. Am. Chem. Soc. 122, 2395–2396 (2000). CAS ISI Article Wilhelms, N., Kuchat, S. & Lehn, J.-M. Organocatalysis of C=N/C=N and C=C/C=N exchange in dynamic covalent chemistry. Helv. Chim. Acta 95, 2635–2651 (2012). ISI Article Khatik, G. L., Kumar, R. & Chakraborti, A. K. Catalyst-free conjugate addition of thiols to α,β-unsaturated carbonyl compounds in water. Org. Lett. 8, 2433–2436 (2006). PubMed Article Hoyle, C. E. & 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 & 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. Additional data 3-Oxo-(N-(4-methyl-2-oxo-2H- chromen-7-yl)-propanoylamide N-(4-Methyl-2-oxo-2H-chromen-7-yl)-acrylamide 3-((2-Aminoethyl)thio)-N-(4-methyl-2-oxo-2H-chromen-7-yl)propanamide npj Genomic Medicine - Open for Submissions Science jobs Science events NatureEvents Directory The 1st Annual Translational Microbiome Conference 14 May 2015 — 15 May 2015 Boston, MA, United States rTMS for depression, OCD and new developments: 2-day rTMS course 19 November 2015 — 20 November 2015 Bijleveldsingel 34, Nijmegen, Netherlands Human Health in the Face of Climate Change: Science, Medicine, and Adaptation 14 May 2015 — 15 May 2015 Carrer d' Isaac Newton, 26, Barcelona, Spain Post a free event More science events Discover more LIF negatively regulates tumour-suppressor p53 through Stat3/ID1/MDM2 in colorectal cancers Nature Communications 17 Oct 2014 Interlocked loops trigger lineage specification and stable fates in the Drosophila nervous system Nature Communications 28 Jul 2014 O-GlcNAc- modification of SNAP-29 regulates autophagosome maturation Nature Cell Biology 24 Nov 2014 Most read Nature.com Open innovation Pavillion Intravenous Sustained Release Drug Delivery Technology Deadline: Mar 21 2015 Reward: $30,000 USD Intravenous delivery allows for the rapid distribution of injected drugs from the veins throughout the entire body. 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.
