de novo macrocyclic peptide ligands for proteins

Protein surfaces that bind to other proteins or to carbohydrates are often broad and shallow, and can thus be difficult to target with small molecules. However, these interactions between carbohydrates and proteins are important in a diverse array of biological processes, many of which have relevance to disease states such as immune disorders, infection, and cancer. An alternative approach to finding ligands to probe or inhibit such interactions is to use peptides, which can better adapt to fit the subtleties of these broad flat binding sites than traditional small molecules. In particular, macrocyclic peptides have the added advantages of increased stability to enzymatic digestion and increased potency. We have shown, through the use of the RaPID system for selection of non-standard peptides, that macrocyclic peptides can bind strongly and selectively to a carbohydrate-active enzyme's catalytic pocket, and thus inhibit its activity. In a proof-of-principle application to human pancreatic alpha amylase, which is the main digestive enzyme at the start of the starch digestive pathway and thus an important enzyme for controlling blood glucose levels in type 2 diabetes, we found a lariat nonapeptide that gives 7 nM inhibition, and was selective over all other glycosidases tested. Work is now underway to expand this first example to other proteins, including other glycosidases, glycosyl transferases, and lectins.