Thermodynamic analysis of protein-ligand interactions of linear tripeptide HCV NS3 protease inhibitors and progress toward the total synthesis of (±)-arboridinine

Interactions between proteins and small molecules dictate an overwhelmingly large number of biological processes, yet our knowledge of the effects of ligand structural changes on the thermodynamics of these interactions is fundamentally lacking. In an effort to expand our understanding of protein-ligand thermodynamics, the binding profiles of a series of linear tripeptide HCV NS3 protease inhibitors were analyzed by ITC. Substituents on the P2 proline residue were examined individually, and important trends were elucidated. The addition of a phenyl group to the 2-position of the heteroaryl subunit of the P2 residue resulted in more favorable binding entropy, which is possibly due to the desolvation of nonpolar surface area. Quinolines without a 2-phenyl substituent were found to bind in an alternate conformation with thermodynamic profiles that were dominated by favorable binding enthalpies rather than entropies. This could possibly be due to a favorable hydrogen bonding interaction between the quinoline nitrogen and Asp81 of the catalytic triad. A series of analogs were prepared to examine the effect of incrementally increasing steric bulk at the P3 side chain of HCV NS3 inhibitors in order to preorganize the ligand into the extended conformation. As steric bulk was increased, the binding affinities improved in turn, notably due to increasingly favorable binding enthalpies along with small gains in entropy. This could possibly attributed to a combination of factors including the entropic benefit derived from preorganization and an enthalpy-driven hydrophobic effect. Several concise synthetic routes were designed toward the total synthesis of the pentacyclic indole alkaloid (±)-arboridinine. A novel Diels-Alder cycloaddition of an indole-3-glyoxamide with a diene to form a key tricyclic intermediate was attempted, but no reaction was observed under a variety of conditions. A second-generation attempt featured attempts at a challenging cascade reaction involving a conjugate addition of an indole-3-glyoxamide into an enone and subsequent attack of an enolate into the intermediate 3,3-disubstituted indolenine. The conjugate addition was successful, providing the first example of indole-3-glyoxamides as substrates for conjugate additions into enones. The resulting indolenine was found to be unreactive under acidic conditions and underwent a retro-Michael reaction to return the indole-3-glyoxamide under basic conditions.