Edward A. Wintner

New promise in combinatorial chemistry: synthesis, characterization, and screening of small-molecule libraries in solution

BACKGROUND The increasing interest in combinatorial chemistry as a tool for the development of therapeutics has led to many new methods of creating molecular libraries of potential lead compounds. Current methods have made it possible to develop libraries of several million compounds. As a result, the limiting factor in the screening of libraries has become the identification and characterization of active species. We have recently described a method for generating libraries of water-soluble compounds containing mixtures of 10(4) to 10(5) different small organic molecules by using generally applicable solution phase chemistry. We set out to develop new methods to characterize and decode these libraries. RESULTS Libraries were generated by condensing a multi-acid-chloride core molecule with various amines, producing molecules with functional groups about a rigid backbone. Composition and complexity of the libraries was evaluated using electrospray mass spectrometry to analyze model libraries containing up to 55 different molecules. The number of peaks obtained in mass spectrometry is directly correlated with the complexity of the library, and we were therefore able to deduce which of the expected compounds had in fact been formed in the library, and which of the building blocks in the library were not efficiently used. An iterative selection procedure was developed using this information, which allowed the screening of libraries of up to 50,000 chemical species to produce a competitive inhibitor of the enzyme trypsin. CONCLUSIONS Our strategy for the identification of active species should be broadly applicable to other methods of generating complex libraries of small molecules. The selection from the library of a compound with desired biological properties augurs well for the potential value of generating and screening complex mixtures of small molecules in solution.

Replication and assembly

Molecules bearing surfaces capable of recognition phenomena can be covalently attached to each other to give self-complementary structures. Such molecules can reveal autocatalytic effects as replicators, and they are able to assemble in a variety of superstructures. Closed-shell assemblies, capable of inclusion phenomena are particularly desirable targets for synthetic and nucleation studies.

A reagent-based strategy for the design of large combinatorial libraries: A preliminary experimental validation

Combinatorial library design can be carried out at either the reagent or the product level. Various reports in the literature have come to conflicting conclusions in favor of one over the other. In this paper a reagent-based screening library design strategy is presented. The method relies on analysis of scaffolds and building blocks separately to define the overall diversity in a compound file. The primary diversity selection by properties relevant for molecular recognition and by redundancy is followed by the application of filters for molecular properties known to be relevant for drug-likeness. Filter properties are rapidly estimated at the product level using a fragmental estimation approach. Initial experimental data suggest that high diversity in vast screening libraries can be achieved by carefully applied reagent level analysis. A potential role of diverse screening libraries in chemical genomics (pharmacological knockouts) is also discussed.