PORTFOLIO

The ability to rapidly isolate specific binding molecules to protein targets is of central importance in drug development. This is generally addressed by the pharmaceutical industry with high-throughput screening of large in-house compound reservoirs (chemical libraries of a size typically smaller than 1 million different compounds).

We have developed an innovative technology, which allows the construction and the simultaneous screening of very large libraries of chemical compounds in a small test tube. This technology relies on the synthesis and screening of libraries of chemical compounds, each carrying a DNA-tag covalently attached as "identification bar code". Since every compound in the library is DNA-encoded (i.e., covalently coupled to a unique oligonucleotidic sequence), library members can be screened in solution at minute concentrations (using biopanning on protein targets immobilized on a solid support). Binders are preferentially recovered and identified by virtue of the corresponding DNA-tags, after PCR amplification.

The Project has been extremely successful, allowing the rapid isolation of low-molecular weight binders to a large variety of protein targets from newly-synthesized encoded libraries, which contain > 1’000’000 individual compounds. We believe that this technology can have a considerable impact on several areas of biomedical research.

The proposed project has the potential to become a break-through methodology for ligand identification and to stimulate industrial activities in the Zürich area and in Switzerland at large. Technology transfer agreements have been finalized between ETH Zurich and Philochem AG, a spin-off biotech company of ETH which is currently in rapid expansion (4500 m2 of industrial building at Otelfingen, 12 employees with the plan to reach 20 by the end of 2010).

We have established the synthetic and DNA-encoding methodologies for the construction of very large DNA-encoded chemical libraries containing > 100’000 compounds.

We have completed the synthesis and characterization of 2 two-building block DNA-encoded chemical libraries, each containing 4’000 compounds.
Furthermore, a three-building block, single-pharmacophore DNA-encoded chemical library containing 1’000'000 compounds was constructed, based on Diels-Alder cycloaddition. The library design represents an extension of our previous work, recently published in Chemistry and Biology.
The libraries have been panned against a multitude of target proteins, both used as a model (streptavidin, albumin, trypsin) and proteins of pharmaceutical relevance (e.g., tumor-associated antigens, metalloproteinases, Bcl-xL, TNF) and have established library decoding methodologies based on 454 and Illumina high-throughput sequencing.

We have been able to identify novel potent binding molecules, notably we have been the first to isolate low molecular weight TNF binders, capable of completely inhibiting TNF-mediated killing of reported tumor cells.

Mannocci, L., Zhang, Y., Scheuermann, J., Leimbacher, M., De Bellis, G., Rizzi, E., Dumelin, C., Melkko, S., Neri, D.: High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries, Proc. Natl. Acad. Sci. USA.105(46):17670-5, 2008;
Buller, F., Mannocci, L., Zhang, Y., Dumelin, C.E., Scheuermann, J., Neri, D.: Design and synthesis of a novel DNA-encoded chemical library using Diels-Alder cycloadditions, Bioorg. Med. Chem. Lett. 18(22), 5926-31, 2008;
Buller, F., Zhang, Y., Scheuermann, J., Schäfer, J., Bühlmann, P., Neri, D.: Discovery of TNF inhibitors from a DNA-encoded chemical library based on diels-alder cycloaddition, Chem Biol. 16(10):1075-86, 2009;
Buller, F., Steiner, M,. Scheuermann, J,. Mannocci, L., Nissen, I., Kohler, M., Beisel, C., Neri, D.: High-throughput sequencing for the identification of binding molecules from DNA-encoded chemical libraries, Bioorg. Med. Chem. Lett. 20(14):4188-92, 2010;
Mannocci, L., Melkko, S., Buller, F., Molnàr, I., Bianké-Gapian, J.P., Dumelin, C.E., Scheuermann, J., Neri, D.: Isolation of potent and specific trypsin inhibitors from a DNA-encoded chemical library, Bioconj. Chem., in press, 2010;
Scheuermann, J., Neri, D.: DNA-encoded chemical libraries: a tool for drug discovery and for chemical biology, ChemBioChem. 11(7):931-7, 2010.

Dario Neri has been the recipient of the Robert-Wenner-Prize of the Swiss Cancer League 2007 and of the Swiss Bridge Award 2008.
Fabian Buller has received the 2008 Award of the Fonds der Schweizerischen Chemischen Industrie (SSCI).