Evaluation of Intrinsic Binding Energy from a Hydrogen Bonding Group in an Enzyme Inhibitor

Abstract

This and two accompanying reports describe the intrinsic binding energy derived from a single hydrogen bond between an inhibitor and an enzyme. The results were obtained by comparing matched pairs of inhibitors of the zinc endopeptidase thermolysin that bind to the enzyme in an essentially identical manner but differ in the presence or absence of a specific hydrogen bond. This report describes five phosphorus-containing analogs of the peptides carbobenzoxy-Gly-Leu-X, in which the Gly-Leu peptide linkage is replaced with a phosphonate ester (-PO2(-)-O-). Values for the inhibition constants of these inhibitors show a direct relation with those of the corresponding phosphonamidate analogs (-PO2(-)-NH- in place of the Gly-Leu peptide moiety), which have been characterized previously as transition state analogs. However, each phosphonate ester is bound about 840 times more weakly than the analogous phosphonamidate, reflecting the loss of 4.0 +/- 0.1 kilocalories per mole in binding energy. From these results and the crystallographic analysis in the next report, it can be inferred that the value of 4.0 kilocalories per mole represents the intrinsic binding energy arising from a highly specific hydrogen binding interaction.

Binding of phosphorus‐containing inhibitors to thermolysin studied by the Poisson‐Boltzmann method

“…It should be noted that these relations are only applicable for inhibitors with minimal size modifications such as Based on Equation 2 and our FDPB results in Table 2, we esZGp(0)LL and ZGP(C)LL, respectively. If AGindirect's are small, our results agree with Bartlett and Marlowe's (1987) estimate that AGH.bond(I)'S are significantly higher than the observed A G, 's.…”

“…The more hydrophilic nature of phosphonamidates is also confirmed in a recent FDPB calculation of CH,-PO,-X-CH,, in addition to early FEP calculations of the inhibitors. Bartlett and Marlowe (1987) and Morgan et al (1991) analyzed the binding mechanism of these inhibitors using Scheme I (Fig. 2).…”

“…The good agreement between the calculations and experiments indicates that the solvation of the inhibitors and the interaction between the X moiety and a hydrogen bond (H-bond) acceptor of the enzyme are two primary determinants of the binding affinity difference. Through a qualitative analysis, Bartlett and Marlowe (1987) suggested that the intrinsic H-bond energy for phosphonamidates Reprint requests to: Jian Shen at his present address: Marion Merre11 Dow, lnc., 2110 East Galbraith Road, P.O. Box 156300, Cincinnati, is significantly higher than the observed binding energy change of 4 kcal/mol from the PI' NH to 0 substitution.…”

Structural Insights Into Translational Fidelity

“…• C), compared to fully-hydrogen-bonded ligands (133,134). In the second position, the density observed for the U·G base pair was most consistent with Watson-Crick rather than wobble geometry (Figure 2e).…”

Phosphonamidate and phosphothioate dipeptides as potential inhibitors of VanX

“…Several studies using thermolysin indicated that phosphonamidate analogues of the peptides bound >800 times stronger than the corresponding phosphonate analogue, due to the fact that the phosphonamidate could form one additional H-bond to the enzyme. 11,12 To probe whether the phosphonamidate analogue of dAla-d-Ala had a similar increase in binding anity to…”