Structure of a retro-binding peptide inhibitor complexed with human alpha-thrombin

Area of Science:

• Biochemistry
• Structural Biology
• Pharmacology

Background:

• Human alpha-thrombin is a key enzyme in blood coagulation.
• Understanding thrombin inhibitor binding is crucial for developing anticoagulants.

Purpose of the Study:

• To determine the crystallographic structure of a ternary complex involving human alpha-thrombin, hirugen, and a peptidyl inhibitor (BMS-183507).
• To elucidate the unique binding mode of the inhibitor to the thrombin active site.

Main Methods:

• X-ray crystallography at 2.6 A resolution.
• Analysis of the ternary complex structure.

Main Results:

• The inhibitor BMS-183507 binds in a novel "retro-binding" mode.
• The inhibitor's N-terminal moiety occupies the primary specificity pocket, with phenyl rings in hydrophobic pockets.
• The inhibitor's backbone forms a parallel beta-strand to thrombin, distinct from natural substrates and previously reported inhibitors.

Conclusions:

• BMS-183507 is the first synthetic inhibitor shown to bind thrombin in a retro-binding fashion.
• This binding mode resembles that of hirudin's N-terminal residues.
• The potent and selective inhibitor (Ki = 17.2 nM) may serve as a template for designing hirudin-based thrombin inhibitors.