α-Fluoro Acid and α-Fluoro Amide Analogs of Acetyl-CoA as Inhibitors of Citrate Synthase: Effect of pK_a Matching on Binding Affinity and Hydrogen Bond Length

An α-fluoro acid analog and an α-fluoro amide analog of acetyl-CoA have been synthesized. The ternary complexes of these inhibitors with oxaloacetate and citrate synthase have been crystallized and their structures analyzed at 1.7 Å resolution. The structures are similar to those reported for the corresponding non-fluorinated analogs (Usher et al., 1994), with all forming unusually short hydrogen bonds to Asp 375. The -fluoro amide analog binds with an affinity 1.5-fold lower than that of a previously described amide analog lacking the -fluoro group. The α-fluoro acid analog binds with a 50-fold decreased affinity relative to the corresponding unfluorinated analog. The binding affinities are consistent with increased strengths of hydrogen bonds to Asp 375 with closer matching of pK_a values between hydrogen bond donors and acceptors. The results do not support any direct correlation between hydrogen bond strength and hydrogen bond length in enzyme-inhibitor complexes.