CCHTS Contents and Abstracts, Vol 1, No. 3

Volume 1, Number 3, 1998: Contents

Combinatorial Libraries: Studies in Molecular Recognition. Pp. 113-126.
H. Peter Nestler and Ruiping Liu
[Abstract]

A Combinatorial Approach To New DNA Minor Groove Binders. Pp. 127-134.
Carsten Behrens and Peter E. Nielsen
[Abstract]

Encoded Chemical Synthesis Coupled to Screening: "Pot Assay". Pp. 135-142.
Z. Parandoosh, S. K. Knowles, X-Y Xiao, C. Zhao, G. S. David and M. P. Nova
[Abstract]

Ratio Encoding Combinatorial Libraries with Stable Isotopes and their Utility in Pharmaceutical Research. Pp. 143-153.
D. S. Wagner, C. J Markworth, C. D. Wagner, F. J. Schoenen, C. E. Rewerts, B. K. Kay and H. M. Geysen
[Abstract]

Abstracts

[Back to top] Combinatorial Libraries: Studies in Molecular Recognition. H. Peter Nestler and Ruiping Liu.
In recent years, combinatorial libraries have become a major tool for drug discovery and drug development. Along the way, one potential use of combinatorial chemistry libraries almost been neglected; the basic study of intermolecular interactions. Especially "one-bead-one-structure" libraries can be a powerful means for the discovery of ligands to synthetic receptors and vice versa. Encoded combinatorial libraries have been used to disclose ligands for well designed macrocyclic host molecules and to elucidate their specificities for peptide sequences. These studies led via receptors with more flexibility to simple host molecules without elaborate design that are accessible to combinatorial synthesis. These findings open a realm of possibilities and applications. An intriguing one is the development of chemical sensors for analytes that are otherwise hard or only unspecifically detected. Furthermore, such libraries and the techniques that were developed to handle them have been used to find new catalysts and enzyme mimics.

In this review we put the emphasis on studies involving "one-bead-one-structure" libraries. We will review the techniques to generate them, to encode and analyze them, and to assay them. We will describe their past usage and the intriguing results of these studies and point out interesting new applications of such libraries for the study of non-covalent intermolecular interactions.

[Back to top] A Combinatorial Approach To New DNA Minor Groove Binders. Carsten Behrens and Peter E. Nielsen.
A combinatorial approach towards new DNA minor groove binders capable of recognizing GC base pairs is reported. From a partly AT - biased library of 5832 different octapeptides of the type Py-Py-X1-X2-X3-Py-Py-gAbu synthesized following the one bead one compound methodology, two compounds containing the central peptide sequences Val-bAla-Tyr and Pip-bAla-Tyr were selected by a fluorescence - double stranded DNA probing assay using the sequence 5'-TTTGTTT-3' as the probe. The two hits were independently synthesized and binding to a recombinant pUC-19 EcoRI/PvuII DNA restriction fragment containing the sequence 5'-TTTGTTT-3' demonstrated. Binding constants to eight targets in the DNA fragment were estimated from quantitative DNAse I footprinting.

[Back to top] Encoded Chemical Synthesis Coupled to Screening: "Pot Assay". Z. Parandoosh, S. K. Knowles, X-Y Xiao, C. Zhao, G. S. David and M. P. Nova.
A variety of screening methodologies is available to identify lead compounds. Screening methods that would permit the direct use of libraries made via the Radiofrequency Encoded Combinatorial chemistry paradigm (each individual small molecule in the library is presented separately on an individual encoded support) have the potential to diminish burdensome steps in this process. Here we report on our studies leading to such a direct method, which we have termed a Pot Assay. Pot Assay is a multiplex assay, which simultaneously measures specific binding of a number of ligands to at least one target. Pot Assay uses specific radiofrequency signals to decode compounds that are high affinity binders. We validated this approach by evaluating the interaction of biotin and its analogs with labeled streptavidin. This report introduces Pot Assay as a rapid, simple, sensitive and accurate format for identifying active members of libraries synthesized on solid supports. The success of this study demonstrates the power of coupling Radiofrequency Encoded Combinatorial chemistry and screening. This assay format may be applied to a wide range of screens that are based on binding events: ligand/receptor, inhibitor/enzyme, antigen/antibody, protein/protein, DNA/protein, and RNA/DNA.

[Back to top] Ratio Encoding Combinatorial Libraries with Stable Isotopes and their Utility in Pharmaceutical Research. D. S. Wagner, C. J Markworth, C. D. Wagner, F. J. Schoenen, C. E. Rewerts, B. K. Kay and H. M. Geysen.
Combinatorial libraries are an important tool for lead discovery in the pharmaceutical industry. Advances in high throughput screening coupled with combinatorial chemistry can significantly reduce the time to find lead compounds. A major difficulty in developing large combinatorial libraries is the ability to identify active compounds. This paper describes a rapid and sensitive encoding/decoding methodology that utilizes stable isotopes and mass spectrometry. The ability of mass spectrometry to precisely determine the intensity of isotopic abundances provides a unique encoding strategy employing synthetically generated ratios of stable isotopes in a compound as the code. The application of ratio encoding is demonstrated using peptoid and imidazole chemistries. Supporting data demonstrate that the incorporation of one or more stable isotopes using unique-predetermined ratios can encode chemical libraries. In addition, the presence of a unique isotopic pattern in a ligand can facilitate the pharmacokinetic analysis. Isotope incorporation into a compound and subsequently into its metabolites reliably distinguishes products from other molecules in the mass spectrum. This is illustrated by metabolic analyses of peptoid and imidazole compounds.