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Automated screening for small organic ligands using DNA-encoded chemical libraries

Nature Protocols volume 11, pages 764–780 (2016)Cite this article

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Abstract

DNA-encoded chemical libraries (DECLs) are collections of organic compounds that are individually linked to different oligonucleotides, serving as amplifiable identification barcodes. As all compounds in the library can be identified by their DNA tags, they can be mixed and used in affinity-capture experiments on target proteins of interest. In this protocol, we describe the screening process that allows the identification of the few binding molecules within the multiplicity of library members. First, the automated affinity selection process physically isolates binding library members. Second, the DNA codes of the isolated binders are PCR-amplified and subjected to high-throughput DNA sequencing. Third, the obtained sequencing data are evaluated using a C++ program and the results are displayed using MATLAB software. The resulting selection fingerprints facilitate the discrimination of binding from nonbinding library members. The described procedures allow the identification of small organic ligands to biological targets from a DECL within 10 d.

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Figure 1: Comparison of different DECL types.
Figure 2: Overview of the screening process.
Figure 3: Plate loading scheme.
Figure 4: Layout of the two-step PCR.
Figure 5: Data processing workflow.
Figure 6: Selection fingerprints.

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Change history

  • 01 April 2016

     In the version of this article initially published online, two of the reference citations were to the wrong references. In addition, incorrect units were given for the final concentration of PBST-biotin. The errors have been corrected for all versions of this article.

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Acknowledgements

This work was supported by ETH Zürich, the Swiss National Science Foundation (SNSF), the Commission for Technology and Innovation (CTI) of the Swiss Confederation, Krebsliga Schweiz/Krebsforschung Schweiz, the European Union's Research and Innovation funding program and Philochem AG. R.M.F. acknowledges a Vizepräsident für Forschung und Wirtschaftsbeziehungen (VPFW)-ETH postdoctoral fellowship endowed by ETH Zürich and Marie-Curie actions. The authors thank S. Melkko, C.E. Dumelin, L. Mannocci, M. Jaggi, M. Leimbacher, M. Steiner, H. Röst, A. Nauer, D. Bajic, M. Valk, S. Biendl and F. Samain for their help with establishing and improving the protocol. The authors thank C. Aquino, L. Poveda and L. Opitz (Functional Genomics Center Zürich) for help with high-throughput DNA sequencing. TruSeq adapter oligonucleotide sequences © 2015 Illumina. All rights reserved. Derivative works created by Illumina customers are authorized for use with Illumina instruments and products only. All other uses are strictly prohibited.

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Author notes

  1. Moreno Wichert, Raphael M Franzini, Fabian Buller, Michael A Stravs & Yixin Zhang

    Present address: Present addresses: Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland (M.W.); Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA (R.M.F.); Covagen AG, Schlieren, Switzerland (F.B.); Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland, and Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland (M.A.S); B CUBE Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany (Y.Z.).,

Authors and Affiliations

  1. Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland

    Willy Decurtins, Moreno Wichert, Raphael M Franzini, Fabian Buller, Michael A Stravs, Yixin Zhang, Dario Neri & Jörg Scheuermann

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Contributions

W.D. established the selection protocol using magnetic beads and the KingFisher magnetic particle processor. W.D., M.W. and R.M.F. applied the protocol and optimized affinity-based selections. W.D. and J.S. optimized the PCR encoding system. F.B. adapted the protocol to use with Illumina sequencing and developed the MATLAB scripts. M.A.S. and Y.Z. wrote and optimized the evaluation software. W.D., D.N. and J.S. wrote the manuscript.

Corresponding authors

Correspondence to Dario Neri or Jörg Scheuermann.

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Competing interests

D.N. is a cofounder and shareholder of Philochem AG and J.S. is a board member of Philochem AG.

Supplementary information

Supplementary Text and Figures

Supplementary Methods 1 and 2, Supplementary Data 1 and Supplementary Note (PDF 951 kb)

Supplementary Software 1

DECL_selection_5w_KF.msz KingFisher program file. It may be adapted upon import into the BindIt software. The BindIt software runs the program on the KingFisher magnetic particle processor. (ZIP 4 kb)

Supplementary Software 2

count.cpp Code of the C++ program “count”. “Count” processes HTDS data using information provided in the structure file and the code lists. (ZIP 8 kb)

Supplementary Software 3

structure.txt Example of a structure file. The structure file provides the C++ program with information about the HTDS data, the code lists as well as the constant regions of the DECL (see Box 2 for further information). (ZIP 0 kb)

Supplementary Software 4

codelist1.txt Example of a code list. The code list contains all the different sequences used in one of the four coding positions. (ZIP 0 kb)

Supplementary Software 5

MATLABscript_2BB.docx MATLAB script 2BB. Selection number and cut-off may be chosen in the highlighted positions. This script provides a 3 dimensional plot for the display of a 2-building block library. Z-axis represents sequence counts. (ZIP 45 kb)

Supplementary Software 6

MATLABscript_3BB.docx MATLAB script 3BB. Selection number and cut-off may be chosen in the highlighted positions. This script provides a 3 dimensional plot for the display of a 3-building block library. Dot colour and size represent sequence counts. (ZIP 64 kb)

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Decurtins, W., Wichert, M., Franzini, R. et al. Automated screening for small organic ligands using DNA-encoded chemical libraries. Nat Protoc 11, 764–780 (2016). https://doi.org/10.1038/nprot.2016.039

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