Abiotic Synthetic Foldamers
Some of the most widely studied protein-protein interactions include those involved in cellular apoptosis. Irregularities associated with the apoptotic pathway can lead to a variety of disorders ranging from cancer to degenerative and autoimmune diseases [57, 58]. Major focus has been placed on the Bcl-2 family of proteins which are key regulators of the apoptotic pathway . In particular, the disruption of the Bcl-xL/Bak complex has been shown to induce apoptosis in unhealthy cells and is therefore a potential target for pharmacological intervention . Fesik and co-workers found that the Bak peptide forms an amphipathic a-helix upon binding into a hydrophobic cleft formed by the BH1, BH2, and BH3 regions of Bcl-xL . Bak projects four hydrophobic side chains (Val74, Leu78, Ile81, and Ile85) along one face of its a-helix into the cleft. Furthermore, alanine scanning experiments suggested that these hydrophobic residues corresponding to the i, i + 4, i + 7, and i + 11 positions on the Bak a-helix are key for complex formation. This information makes possible the design of Bak mimetics that can potentially bind to Bcl-xL.
Hamilton and co-workers have recently reported a novel trispyridylamide fol-damer that inhibits the Bcl-xL/Bak interaction (Fig. 7.13a) . This scaffold was designed to mimic the i, i + 4, and i + 7 residues of the BH3 domain of Bak. A stabilizing bifurcated hydrogen-bonding network allows 18 to adopt a preferred
conformation in which all three R-functional groups are projected on the same face of the molecule. Overlay of a minimized energy conformation of 18 with the a and b positions of the i, i + 4, and i + 7 methyl groups of a poly-alanine a-helix shows close correspondence of the two structures with an RMSD = 0.94 A (Fig. 7.13 b, c). The overall conformation of the backbone and the position of the side chain functional groups predicted by MM2 minimization calculations were confirmed in the solid state by an X-ray crystal structure of a nitro derivative of 18. In addition, 1H NMR studies including concentration and temperature dependence experiments were performed to study the stability and hydrogen-bonding pattern in 18. These experiments suggested that the amide proton is intramolec-ularly hydrogen bonded in solution both in polar and nonpolar solvents as well as in the solid state.
A competitive binding fluorescence polarization (FP) assay was used to determine the ability of derivatives of 18 to disrupt the Bcl-xL/Bak complex. Inhibition constants (Ki) in the low micromolar range were found for the trispyridy-lamide foldamers. The best inhibitor had a side chain substitution pattern of R1, R2 = Bn, and R3 = iPr and a Ki value of 1.6 mM. Differences in the binding affinities were observed when the R-groups were varied. For instance, the derivative with three R = Bn substituents had a Ki value greater than 20 mM, emphasizing the importance of surface complementarity and the selectivity that can be gained by the variation of side chains.
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