| Protein--protein interactions (PPIs) are essential components in cellular signaling pathways as well as important viral processes such as infection, replication, and immune suppression. The many uncharacterized PPIs involved in such interaction networks often represent compelling therapeutic drug targets. To date, however, the main strategies for discovery of small molecule modulators of PPIs are limited to structurally characterized targets. Recent developments in peptide secondary structure mimetics have yielded effective designs, however, very few screening libraries of such mimetics currently exist that can be used to interrogate PPI targets. We initiated a program to prepare a comprehensive small molecule library designed to mimic the three major recognition motifs that mediate PPIs (alpha-helix, beta-turn, beta-strand). Three libraries built around templates designed to mimic each such secondary structure and substituted with all triplet combinations of groups representing the 20 natural amino acid side chains would contain a member capable of mimicking the key interaction residues of most targetable PPIs. We present herein the results of the design, synthesis, and validation of an 8,000 member alpha-helix mimetic library and a 4,200 member beta-turn mimetic library. The screening of these libraries is expected not only to provide lead structures against alpha-helix- or beta-turn-mediated interactions, even if the nature of the interaction is unknown, but also yield key insights into the recognition motif (alpha-helix or beta-turn), and identify the key residues mediating the interaction. Consistent with this expectation, screening of the libraries against p53/MDM2 and HIV-1 gp41 (alpha-helix mimetic library) or the opioid receptors (beta-turn mimetic library) led to the discovery of library members that mimic the known endogenous ligands. These efforts led to the discovery of high affinity alpha-helix mimetics (Ki = 0.7 muM) against HIV-1 gp41 as well as high affinity and selective beta-turn mimetics (K i = 80 nM) against the kappa-opioid receptor. The studies herein suggest that the use of such comprehensive libraries of peptide secondary structure mimetics, built around effective molecular scaffolds, constitutes a powerful method of interrogating PPIs, providing small molecule modulators of PPI networks for therapeutic target validation, lead compound discovery, and identification of modulators of biological processes for study. |
