Ligand discovery

The field of synthetic enzyme models encompasses attempts to prepare enzymelike functional macromolecules by chemical synthesis [30]. One particularly relevant approach to such enzyme mimics concerns dendrimers, which are treelike synthetic macromolecules with a globular shape similar to a folded protein, and useful in a range of applications including catalysis [31]. Peptide dendrimers, which, like proteins, are composed of amino acids, are particularly well suited as mimics for proteins and enzymes [32]. These dendrimers can be prepared using combinatorial chemistry methods on solid support [33], similar to those used in the context of catalyst and ligand discovery programs in chemistry [34]. Peptide dendrimers used multivalency effects at the dendrimer surface to trigger cooperativity between amino acids, as has been observed in various esterase enzyme models [35]. 

While tractability for screening and ligand discovery has been demonstrated for these enzymes, significant challenges remain, notably in identifying chemotypes that show potent and selective inhibition of isoforms of interest while retaining physicochemical properties suitable for the intracellular site of action. 

George M. Whitesides is Mallinckrodt Professor of Chemistry at Harvard University. He received his A.B. from Harvard College in 1960 and his Ph.D. from the California Institute of Technology in 1964. His research areas are Materials Science and Organic Chemistry, with specific focus in surface chemistry, materials science, self-assembly, capillary electrophoresis, organic solid state, molecular virology, directed ligand discovery, and protein chemistry. He is a member of the National Academy of Sciences, and he received the U.S. National Medal of Science in 1998. 

Howard, A. D., McAllister, G., Feighner, S. D., et al. (2001) Orphan G-protein-coupled receptors and natural ligand discovery. Trends Pharmacol. Sci. 22, 132-140. 

Frontal Affinity Chromatography - Mass Spectrometry for Ligand Discovery and Characterization... 

Mass spectrometry enables the type of direct analyses described, but it does have its limitations. Online operation forces detection at infusion concentrations, in salty buffer and under complex mixture conditions. General ion suppression results from the buffer and mixture components, and mixture complexity can tax the resolution of even the best mass spectrometers. Increasing compound concentration is not the answer, as this leads to problems of solubility and increased compound consumption. We have found that the online method can work successfully for up to 100 compounds per analysis, but the false negative rate becomes appreciable [21]. As an alternative for ligand discovery purposes, we have developed a FAC-LC/MS system in which FAC effluent is sampled and analyzed by LC/MS [19]. This system offers the ability to concentrate mixture components and introduces another dimension to the data in order to tolerate more complex mixtures (Fig. 6.9). Using this system, we have screened approximately 1000 modified trisaccharide acceptor analogs targeting immobilized N-... 

More recently, Brennan has shown that FAC-MALDI-MS can be used to screen small molecules, relying upon MRM transitions to overcome the chemical noise generated by the matrix [16]. This is an acceptable approach for known compounds, but for ligand discovery from uncharacterized mixtures, ion selection... 

Mazitschek, R., Patel, V., Wirth, D.F. and Clardy, J. (2008) Development of a fluorescence polarization based assay for histone deacetylase ligand discovery. Bioorganic Medicinal Chemistry Letters, 18, 2809-2812. 

A. Giannis, T. Kolter, Peptidomimetics for receptor ligands—Discovery, development, and medical perspectives, Angew. Chem. Int. Ed. 32(9) (1993) 1244—1267. 

E. M., Wells, J. A. (2000) Site-directed ligand discovery. Proc Natl Acad Sci U SA97, 9367-9372. 

Giannis A and Kolter T (1993) Peptidomimetics for receptor ligands - Discovery, development, and medicinal perspectives. Angew Chem Int Edn Engl 32, 1244-1267. 

Vanwetswinkel, S., et al., TINS, target immobilized NMR screening an efficient and sensitive method for ligand discovery. Chem Biol, 2005, 12, 207-216. 

Stahl, M. T., Nicholls, A., Sayle, R. A. and Grant, J. A. (1999). Rapid conformation search applied to ligand discovery. Book of Abstracts, 217th ACS National Meeting, Anaheim, CA, 21-25 March 1999, COMP-026. 

Application of TINS to Ligand Discovery 6.4.1 Soluble Targets... 

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