Structures of two thermolysin-inhibitor complexes that differ by a single hydrogen bond

Area of Science:

• Enzyme kinetics and structural biology
• Protein-ligand interactions
• Metalloprotease inhibition

Background:

• Thermolysin is a metalloprotease implicated in various biological processes.
• Understanding enzyme-inhibitor interactions is crucial for drug design.
• Peptide and ester analogs can serve as probes for binding mechanisms.

Purpose of the Study:

• To determine the binding mode of an ester analog of Cbz-GlyP-(O)-Leu-Leu to thermolysin.
• To compare the binding mode and energy of the ester analog with its peptide counterpart, Cbz-GlyP-(NH)-Leu-Leu.
• To elucidate the role of a specific hydrogen bond in enzyme-inhibitor binding.

Main Methods:

• X-ray crystallography was employed to determine the three-dimensional structures of enzyme-inhibitor complexes.
• Comparative analysis of atomic coordinates to assess structural differences between the ester and peptide analog complexes.
• Calculation of intrinsic binding energy differences.

Main Results:

• The binding mode of the ester analog (Cbz-GlyP-(O)-Leu-Leu) to thermolysin is virtually identical to the peptide analog (Cbz-GlyP-(NH)-Leu-Leu), with a maximum difference of 0.2 angstroms.
• The two enzyme-inhibitor complexes exhibit a significant difference in intrinsic binding energy (4.1 kilocalories per mole).
• The primary difference between the two complexes is the presence or absence of a specific hydrogen bond involving the inhibitor.

Conclusions:

• The ester analog serves as a valid structural mimic of the peptide analog in thermolysin binding.
• A single hydrogen bond significantly contributes to the binding energy of thermolysin inhibitors.
• These findings provide insights into the design of potent and selective metalloprotease inhibitors.