Combinatorial synthesis of beta-peptides with microwave irradiation: Toward the discovery and development of protein-protein interaction inhibitors

The desire to develop a treatment or cure for human illness drives both science and scientists throughout the world. The challenge of inhibiting protein-protein interactions has created an opportunity for the development of new strategies that depart from traditional medicinal chemistry, as exemplified by investigation of the p53/MDM2 interaction. One successful strategy has been the creation of proteomimetic scaffolds called foldamers, which include beta-peptides. The predictable relationship between beta-amino acid sequence and folding has inspired several biological applications of beta-peptides, including the inhibition of protein-protein interactions. For many such applications it would be desirable to prepare and screen large beta-peptide libraries. However, standard solid-phase peptide synthesis (SPPS) protocols are not efficient enough to support a library approach for some types of beta-peptides. The work described in this Thesis demonstrates how the development of microwave-assisted combinatorial synthesis of beta-peptides has facilitated the discovery and development of biologically active foldamers. The effects of microwave irradiation on the solid-phase synthesis of beta-peptides were evaluated, identifying a clear benefit from microwave irradiation for longer beta-peptides and achieving a 10-fold reduction in synthesis time. Using microwave-assisted methodology, high-quality beta-peptide combinatorial libraries were rapidly prepared via both split-and-mix techniques on polystyrene (PS) macrobeads and in parallel using 96-well filter plates. Libraries were designed, prepared, and screened as part of an effort to identify and optimize foldamer inhibitors of several protein-protein interactions, including p53/MDM2, Bcl-xL/Bak, and transforming growth factor beta3/type II receptor and the neurokinin B/neurokinin receptor peptide/protein interaction. The utility of beta-amino acids in medicinal chemistry via a beta-scan was investigated. Split-and-mix and parallel synthesis techniques were compared to determine when and how to apply each method. Large-scale synthesis of important beta-amino acids and efforts toward stabilization of a proteomimetic scaffold are described. In summary, this Thesis describes initial efforts toward the discovery and development of foldamer inhibitors for protein-protein interactions using structure-guided design as a starting point for the rapid and efficient searching of chemical space via microwave-assisted synthesis.