Combinatorial chemistry reveals a new motif that binds the platelet fibrinogen receptor, gpIIbIIIa

In situ synthesis of peptide microarrays using ink-jet microdispensing

The study of protein-protein and protein-DNA interactions is critical to understand biological processes. This article presents the methodology to create peptide microarrays in situ for the high-throughput screening of complex biomolecules. The in situ ink-jet peptide synthesis results in a conservation of costly reagent and amino acids, whereas providing a means to produce denser peptide arrays. A smaller amount of test sample is required to observe interaction when using these high-density peptide arrays.

Chemical Characterization of α-Oxohydrazone Ligation on Colloids: toward Grafting Molecular Addresses onto Biological Vectors

New mild and specific chemical strategies have been developed recently for the selective coupling of biological macromolecules. Among them, the hydrazone ligation strategy offers high chemoselectivity and versatility. We intended to use hydrazone ligation to target the controlled release of therapeutic agents by biological vectors (multilamellar vesicles called onion vectors). An accurate measure of ligation bond stability was needed to ensure that the ligation bond would stand long exposures to physiological conditions. In this study, we have completed a kinetic and thermodynamic characterization of hydrazone formation on a model reaction. The mechanism of the reaction in solution as well as in different self-organized systems (micelles, liposomes and multilamellar vesicles) was investigated. In solution, submicromolar stability was achieved as well as half-lives of several weeks. The kinetics and stability were both enhanced in colloidal media thanks to autoassociation effects. The results were expanded to the realistic case of RGD-peptide coupling to onion vectors. The RGD grafted onion vectors were then tested for their ability to bind endothelial cells in vitro.

Combinatorial approaches to inhibitors of VLA-4: piperazine-peptoid-bisarylureas

A combinatorial approach towards identifying inhibitors of VALA-4 was investigated. A library of piperazine-peptoid-bisarylureas was assembled in solid phase and screening in the novel v-well assay enabled the identification of active compounds.

Non-natural CBP2 binding peptides and peptomers modulate carcinoma cell adhesion and invasion

A combinatorial approach that utilized a repertoire of bacteriophage-peptides has identified a number of non-natural CBP2 binding peptides. Moreover, co-localization of some of these peptides with CBP2 in a number of tumor cell lines demonstrated that the peptides were directed to an intracellular location spatially coincident with the normal distribution of CBP2 [Sauk et al., 2000]. From among these sequences WHYPWFQNWAMA and LDSRYSLQAAMY were the most effective CBP2 binding peptides and best fulfilled the combinatorial motif containing deep hydrophobic pockets. When the hydropathic profiles of collagen alpha1(IV) and alpha2 (IV) were compared with these dodecapeptides, the hydropathic profiles of WHYPWFQNWAMA and LDSRYSLQAAMY closely matched those of alpha1(IV) 414-452 and alpha1(IV)531-543. These peptides were shown to be functional peptidomimics and possessed the ability to alter cell adhesion and invasion of human squamous cell carcinoma cell lines. Peptomers were formed of these non-natural peptides to explore the role that a repetitive peptide may have on cell adhesion. The enhanced cell adhesion observed with the peptomers required both CBP2 antibodies and integrin antibodies for inhibition. The enhanced adhesion observed even in the face of combined antibody inhibition was consistent with such complexes possessing correspondingly slower dissociation rates. Thus, suggesting that peptomers may function in a like manner to multimeric peptide MHC complexes (tetramers) binding more than one cell receptor on a specific cell. These findings evoke both peptidomimics of native ligands and their peptomers as potential reagents by which to target tumor cells for chemotherapy, imaging, or retargeting viral vectors for gene therapy.

Rapid identification of substrates for novel proteases using a combinatorial peptide library

Fluorogenic substrates for assaying novel proteolytic enzymes could be rapidly identified using an easy, solid-phase combinatorial assay technology. The methodology was validated with leader peptidase of Escherichia coli using a subset of an intramolecularly quenched fluorogenic peptide library. The technique was extended toward the discovery of substrates for a new aspartic protease of pharmaceutical relevance (human napsin A). We demonstrated for the first time known to us that potent fluorogenic substrates can be discovered using extracts of cells expressing recombinant enzyme to screen the peptide library. The straightforward and rapid optimization of protease substrates greatly facilitates the drug discovery process by speeding up the development of high throughput screening assays and thus helps more effective exploitation of the enormous body of information and chemical structures emerging from genomics and combinatorial chemistry technologies.

Combinatorial chemistry defines general properties of linkers for the optimal display of peptide ligands for binding soluble protein targets to TentaGel microscopic beads

Affinity chromatography and the binding of soluble target proteins to novel or known ligands attached to solid supports are important phenomena to basic and applied research. Satisfactory display of a ligand for the acceptor protein is critical for successful binding to occur. Here we describe the application of combinatorial chemistry to systematically explore the properties of linkers used to present peptide ligands to various protein targets. Our main interest is in drug discovery, and our results probably explain, in large part, the disappointing efficiency of an early drug discovery method known as the "Selectide Process" (Lam, K. S., et al. (1991) Nature 358, 82-84). Interestingly, for all seven protein targets studied, a cationic feature was found to be a common theme for optimal linkers displaying peptide ligands on TentaGel beads, and this is not likely to be caused by ionic exchange mechanisms.