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Encoded self-assembling chemical libraries


The isolation of molecules capable of high-affinity and specific binding to biological targets is a central problem in chemistry, biology and pharmaceutical sciences. Here we describe the use of encoded self-assembling chemical (ESAC) libraries for the facile identification of molecules that bind macromolecular targets. ESAC technology uses libraries of organic molecules linked to individual oligonucleotides that mediate the self-assembly of the library and provide a code associated with each organic molecule. After panning ESAC libraries on the biomolecular target of interest, the 'binding code' of the selected compounds can be 'decoded' by a number of experimental techniques (e.g., hybridization on oligonucleotide microarrays). The potential of this technology was demonstrated by the affinity maturation (>40-fold) of binding molecules to human serum albumin and bovine carbonic anhydrase, leading to binders with dissociation constants in the nanomolar range.

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Figure 1: Schematic representation of ESAC libraries.
Figure 2: Decoding of model ESAC selections against streptavidin.
Figure 3: Microarray decoding of ESAC affinity maturation selections against HSA and CA.
Figure 4: Affinity measurements of ligands to HSA and CA, obtained by ESAC selections.
Figure 5: Isothermal titration calorimetry profiles of CA binders.


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This work was supported by the ETH Zürich, the Swiss National Science Foundation, the Bundesamt für Bildung und Wissenschaft/EU (STROMA Project) and Philogen. S.M. has been the recipient of a Boehringer-Ingelheim bursary and of an ETH Zürich bursary (special grant: ESACHEL). C.E.D. is a recipient of a bursary from the Roche Research Foundation. We are grateful to J. Sobek and R. Schlapbach for access to instrumentation and help with the microarray technology, and to R. Brunisholz, W. Amrein, O. Scheidegger, O. Greter, P. Hunziker and S. Chesnov for analytical assistance. We thank G. Guarda for help in decoding by sequencing, and R. Buff, O. Schärer and members of the Neri group for helpful discussions.

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Correspondence to Dario Neri.

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Competing interests

ESACHEL technology is covered by a patent application, which was licensed from ETH Zurich to Philogen S.r.l. under a share of revenues agreement. D.N. owns shares of Philogen and consults for this company. Since August 2003, S.M. and J.S. have received a salary from Philogen. The company also pays for reagents and overhead for ETH Zurich.

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Melkko, S., Scheuermann, J., Dumelin, C. et al. Encoded self-assembling chemical libraries. Nat Biotechnol 22, 568–574 (2004).

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