High-throughput sequencing for the identification of binding molecules from DNA-encoded chemical libraries.

DNA-encoded chemical libraries are large collections of small organic molecules, individually coupled to DNA fragments that serve as amplifiable identification bar codes. The isolation of specific binders requires a quantitative analysis of the distribution of DNA fragments in the library before and after capture on an immobilized target protein of interest. Here, we show how Illumina sequencing can be applied to the analysis of DNA-encoded chemical libraries, yielding over 10 million DNA sequence tags per flow-lane. The technology can be used in a multiplex format, allowing the encoding and subsequent sequencing of multiple selections in the same experiment. The sequence distributions in DNA-encoded chemical library selections were found to be similar to the ones obtained using 454 technology, thus reinforcing the concept that DNA sequencing is an appropriate avenue for the decoding of library selections. The large number of sequences obtained with the Illumina method now enables the study of very large DNA-encoded chemical libraries (>500,000 compounds) and reduces decoding costs.

[1]  Joakim Lundeberg,et al.  Generations of sequencing technologies. , 2009, Genomics.

[2]  Christoph E. Dumelin,et al.  Selection of streptavidin binders from a DNA-encoded chemical library. , 2006, Bioconjugate chemistry.

[3]  Samuel E. Fox,et al.  Applications of ultra-high-throughput sequencing. , 2009, Methods in molecular biology.

[4]  Harald Schwalbe,et al.  Perspectives on NMR in drug discovery: a technique comes of age , 2008, Nature Reviews Drug Discovery.

[5]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , 1997 .

[6]  Christoph E. Dumelin,et al.  Encoded self-assembling chemical libraries , 2004, Nature Biotechnology.

[7]  Lars Kolster Petersen,et al.  A yoctoliter-scale DNA reactor for small-molecule evolution. , 2009, Journal of the American Chemical Society.

[8]  P. Harbury,et al.  Synthetic ligands discovered by in vitro selection. , 2007, Journal of the American Chemical Society.

[9]  Dalia Cohen,et al.  Functional genomics to new drug targets , 2004, Nature Reviews Drug Discovery.

[10]  D. Neri,et al.  Isolation and characterization of human monoclonal antibodies specific to MMP-1A, MMP-2 and MMP-3. , 2010, Experimental cell research.

[11]  György M. Keserü,et al.  The influence of lead discovery strategies on the properties of drug candidates , 2009, Nature Reviews Drug Discovery.

[12]  Christopher L. McClendon,et al.  Reaching for high-hanging fruit in drug discovery at protein–protein interfaces , 2007, Nature.

[13]  Corey Nislow,et al.  Combination chemical genetics. , 2008, Nature chemical biology.

[14]  Peter Bühlmann,et al.  Discovery of TNF inhibitors from a DNA-encoded chemical library based on diels-alder cycloaddition. , 2009, Chemistry & biology.

[15]  Christof Baltes,et al.  A portable albumin binder from a DNA-encoded chemical library. , 2008, Angewandte Chemie.

[16]  David R. Liu,et al.  Translation of DNA into a library of 13,000 synthetic small-molecule macrocycles suitable for in vitro selection. , 2008, Journal of the American Chemical Society.

[17]  Lorenz M Mayr,et al.  Novel trends in high-throughput screening. , 2009, Current opinion in pharmacology.

[18]  Dario Neri,et al.  Design and synthesis of a novel DNA-encoded chemical library using Diels-Alder cycloadditions. , 2008, Bioorganic & medicinal chemistry letters.

[19]  M. Marra,et al.  Applications of next-generation sequencing technologies in functional genomics. , 2008, Genomics.

[20]  G. Turcatti,et al.  Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. , 2000, Nucleic acids research.

[21]  C. Lipinski.  Drug-like properties and the causes of poor solubility and poor permeability. , 2000, Journal of pharmacological and toxicological methods.

[22]  Baoguang Zhao,et al.  Design, synthesis and selection of DNA-encoded small-molecule libraries. , 2009, Nature chemical biology.

[23]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[24]  Samu Melkko,et al.  DNA-encoded chemical libraries for the discovery of MMP-3 inhibitors. , 2008, Bioconjugate chemistry.

[25]  Clive Brown,et al.  Toward the $1000 human genome , 2005 .

[26]  R. Lerner,et al.  Encoded combinatorial chemistry. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[27]  G. Winter,et al.  Making antibodies by phage display technology. , 1994, Annual review of immunology.

[28]  David R. Liu,et al.  DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles , 2004, Science.

[29]  Christoph E. Dumelin,et al.  High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries , 2008, Proceedings of the National Academy of Sciences.

[30]  Christoph E. Dumelin,et al.  Isolation of high-affinity trypsin inhibitors from a DNA-encoded chemical library. , 2007, Angewandte Chemie.

[31]  Samu Melkko,et al.  DNA-encoded chemical libraries , 2022, Nature Reviews Methods Primers.