Probing the abilities of synthetically useful serine proteases to discriminate between the configurations of remote stereocenters using chiral aldehyde inhibitors

The abilities of the synthetically useful serine proteases, subtilisin Carlsberg (SC) and alpha-chymotrypsin (CT), to discriminate between R- and S-configurations of stereocenters remote from the catalytic site have been explored using chiral aldehyde transition state analog inhibitors as probes. The inhibitors evaluated were (R)- and (S)-3-phenylbutanal and (R)- and (S)-4-phenylpentanal, for which the stereocenters at C-3 and C-4 respectively are distant from the aldehyde functionality that interacts with the catalytic serine residue. The achiral parent compounds, 3-phenylpropanal and 4-phenylbutanal, respectively, were also assessed for reference purposes. Each aldehyde was found to be a competitive inhibitor for both enzymes, with CT being significantly more potently inhibited than SC. Within this series, the presence of an R-center methyl group improved binding significantly over that of the achiral parent aldehyde for both enzymes. In contrast, the effects on binding of S-methyl substituents in the same positions were modest, and generally somewhat deleterious. Furthermore, the greater the separation of the stereocenter from the aldehyde group, the lower the degree of configuration discrimination. The most effective inhibition, and the highest degree of remote stereocenter discrimination, observed was that by CT of (R)-3-phenylbutanal, whose K-I of 8.4 mu M was 61-fold lower than that of its achiral parent 3-phenylpropanal, and ss-fold lower than the K-I of its S-enantiomer. Molecular mechanics and molecular dynamics calculations were performed to identify each favored aldehyde-enzyme complex and to reveal the binding and orientation differences responsible for the R- and S-enantiomer binding discriminations observed.