Search for a command to run...
The folded 3D structures of peptides and proteins provide excellent starting points for the design of synthetic molecules that mimic key epitopes (or surface patches) involved in protein−protein and protein−nucleic acid interactions. Protein epitope mimetics (PEMs) may recapitulate not only the structural and conformational properties of the target epitope but also their biological activities. By transferring the epitope from a recombinant to a synthetic scaffold that can be produced by parallel combinatorial methods, it is possible to optimize properties through iterative cycles of library synthesis and screening, and even to evolve new biological activities. One very interesting scaffold is found in β-hairpin motifs, which are used by many proteins to mediate molecular recognition events. This motif is readily amenable to PEM design, for example, by transplanting hairpin loop sequences from folded proteins onto hairpin-stabilizing templates, such as the dipeptide d-Pro-l-Pro. In addition, β-hairpin peptidomimetics can also be exploited to mimic other types of epitopes, such as those based on α-helical secondary structures. The size and shape of β-hairpin PEMs appear well suited for the design of inhibitors of both protein−protein and protein−nucleic acid interactions, endeavors that have so far proven difficult using small “drug-like” molecules. In recent work, it was shown that β-hairpin PEMs can be designed that mimic the canonical conformations of antibody hypervariable loops, suggesting that novel small-molecule antibody mimics may be feasible. Using naturally occurring peptides as starting points, β-hairpin mimetics have been discovered that possess antimicrobial activity, while others are potent inhibitors of the chemokine receptor CXCR4. β-Hairpin PEMs have also been designed and optimized that mimic an α-helical epitope in p53 and so block its interaction with HDM2. A crystal structure of one HDM2−mimetic complex revealed how the surface of the protein had adapted to the shape of the hairpin, thereby enhancing inhibitor affinity. Small folded RNA motifs also make interesting targets for inhibitor design. For example, β-hairpin mimetics have been designed and optimized that bind with high affinity and good selectivity to the TAR and RRE RNA motifs from HIV-1. Solution structures of the mimetics both free and bound to the RNA target provided some surprises, as well as an improved understanding of the mechanisms of binding. These mimetics represent still a relatively new family of RNA-binding molecules, but clearly one with potential for development into novel antiviral agents.