Encoded self-assembling chemical libraries (ESACHEL)

Abstract

The invention concerns a chemical compound comprising a chemical moiety (p) capable of performing a binding interaction with a target molecule (e.g. a biological target) and further comprising an oligonucleotide (b) or functional analogue thereof. In a first embodiment according to the invention, the chemical compound is characterized in that the oligonucleotide (b) or functional analogue comprises at least one self-assembly sequence (b1) capable of performing a combination reaction with at least one self-assembly sequence (b1') of a complentary oligonucleotide or functional analogue bound to another chemical compound comprising a chemical moiety (q). In a second embodiment according to the invention, the chemical compound which comprises a coding sequence (b1) coding for the identification of the chemical moiety (p) is characterized in that the chemical compound further comprises at least one self-assembly moiety (m) capable of performing a combination reaction with at least one self-assembly moiety (m') of a similar chemical compound comprising a chemical moiety (q). The invention comprises corresponding libraries of chemical compounds as well as methods of biopanning of target molecules and of identifying such targets.

Description

ASSOCIATED APPLICATION DATA[0001] This application claims priority of the U.S. Provisional Application No. 60 / 362,599 filed on Mar. 8, 2002 and of the international application PCT / EP 02 / 04153 filed on Apr. 15, 2002.ABSTRACT[0002] 1. Problem to be Solved[0003] The isolation of specific binding molecules (e.g. organic molecules) is a central problem in chemistry, biology and pharmaceutical sciences. Typically, millions of molecules have to be screened, in order to find a suitable candidate. The preparation of very large libraries of organic molecules is typically cumbersome. Furthermore, the complexity associated with the identification of specific binding molecules from a pool of candidates grows with the size of the chemical library to be screened.[0004] 2. Solution[0005] In this invention, we use self-assembling libraries of organic molecules (typically forming dimers, trimers or tetramers), in which the organic molecules are linked to an oligonucleotide which mediates the self-as...

AI Technical Summary

Benefits of technology

0086] Some of the contributions of ESACHEL technology for the identification of specific binders are related to a chemical process, termed the "chelate effect". The term chelate was first applied in 1920 by Sir Gilbert T. Morgan and H. D. K. Drew [J. Chem. Soc., 1920, 117, 1456], who stated: "The adjective chelate, derived from the great claw or chela (chely- Greek) of the lobster or other crustaceans, is suggested for the caliper-like groups which function as two associating units and fasten to the central atom so as to produce heterocyclic rings."

0087] The chelate effect can be seen by comparing the reaction of a chelating ligand and a metal ion with the corresponding reaction involving comparable monodentate ligands. For example, comparison of the binding of 2,2'-bipyridine with pyridine or 1,2-diaminoethane (ethylenediamine) with ammonia. It has been known for many years that a comparison of this type always shows that the complex resulting from coordination with the chelating ligand is much more thermodynamically stable.

0088] Let us consider the dissociation steps of a monodentate ligand, compared to multidentate (e.g., bidentate ligands). When a monodentate group is displaced, it is lost into the bulk of the solution. On the other hand, if one end of a bidentate group is displaced the other arm is still attached and it is only a matter of the arm rotating around and it can be reattached again (FIG. 8). In general, the formation of the complex with bidentate groups is favored, compared to the complex with the corresponding monodentate groups.

0089] The chelate effect has been shown to be able to contribute to high-affinity binding not only in the case of multidentate metal ligands, but in many other chemical situations, including binding interactions with macromolecules (e.g., multidentate DNA binding, chelating recombinant antibodies) [Neri D, Momo M, Prospero T, Winter G. High-affinity antigen binding by chelating recombinant antibodies (CRAbs). J Mol Biol. (1995) 246:367-73].

0090] When examining some ESACHEL embodiments, for example those in which two chemical moieties are oligomerized by means of DNA heteroduplex formation, it is useful to illustrate the chelate effect in the context of the stability of the DNA heteroduplex which bridges the two chemical entities involved in the specific binding interaction with a target. In most cases, it will be convenient to have heteroduplexes (or triplexes or quadruplexes) which de facto do not dissociate in the experimental conditions chosen for the ESACHEL biopanning. Useful information and a discussion on the energetics of cooperative binding with short DNA heteroduplex fragments (8 bp) can be found in Distefano and Dervan, 1993 [Distefano M D, Dervan P B. Energetics of cooperative binding of oligonucleotides with discrete dimerization domains to DNA by triple helix formation Proc Natl Acad Sci USA. (1993) 90: 1179-1183.].

Problems solved by technology

Utilizing the code C for the identification of the polymer A and attaching the code C to the polymer A with a linker molecule B allows the polymer to be identified exactly, however, the solution presented in U.S. Pat. No. 5,573,905 (which basically is the same as published by Brenner and Lerner, 1992) is limited to this special type of a chemical moiety.

The fact that individual synthesis has to be carried out for each individual of a chemical library is regarded as another disadvantage.

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