SuperMimic – Fitting peptide mimetics into protein structures

BACKGROUND: Various experimental techniques yield peptides that are biologically active but have unfavourable pharmacological properties. The design of structurally similar organic compounds, i.e. peptide mimetics, is a challenging field in medicinal chemistry. RESULTS: SuperMimic identifies compounds that mimic parts of a protein, or positions in proteins that are suitable for inserting mimetics. The application provides libraries that contain peptidomimetic building blocks on the one hand and protein structures on the other. The search for promising peptidomimetic linkers for a given peptide is based on the superposition of the peptide with several conformers of the mimetic. New synthetic elements or proteins can be imported and used for searching. CONCLUSION: We present a graphical user interface for finding peptide mimetics that can be inserted into a protein or for fitting small molecules into a protein. Using SuperMimic, promising locations in proteins for the insertion of mimetics can be found quickly and conveniently

Development of a Murine Model to Study Inhibitors of CXCR3-Ligand Interactions

CXCR3 is involved in numerous inflammatory disorders such as rheumatoid arthritis, multiple sclerosis, allograft rejection and inflammatory bowel disease. There is a strong and growing demand for novel and effective therapeutics that can mediate CXCR3 activity. In this study, a set of botanical compounds and a peptide mimetic of the second extracellular loop (ECL-2) of CXCR3 were examined for the ability to inhibit interactions between CXCR3 and its ligands in a murine model. EGCG, a green tea polyphenol, and gallotannin, derived from many plant sources, strongly inhibited the chemotaxis of stably transfected murine CXCR3-expressing L1.2 cells in response to murine CXCL9, CXCL10, and CXCL11. EGCG was also shown to bind directly to murine CXCR3 ligands with high affinities. Baicalin, a flavonoid found in the medicinal plant Scutellaria baicalensis, and ginkgolide A, from the Ginkgo biloba tree, did not significantly reduce cell migration towards murine CXCR3 ligands, nor did the peptide mimetic of the ECL-2 of murine CXCR3. Other green tea polyphenols similar in structure to EGCG were also analyzed and were less able to inhibit murine CXCR3 ligand-mediated chemotaxis than EGCG, with the following efficacies: ECG > EGC > EC. It was observed that the most effective test compounds contained more hydroxyl groups and hence were more negatively charged, similar to glycosaminoglycans, which are extracellular matrix components that bind many chemokines. It is possible that EGCG and gallotannin are able to bind the GAG-binding domains of murine CXCR3 ligands, which allows them to prevent receptor binding and inhibit their function. This possibility represents the public health relevance of this research, as EGCG and gallotannin may be attractive candidates as lead compounds for new therapeutics for CXCR3-mediated and other inflammatory diseases