Selective boron-containing thrombin inhibitors--X-ray analysis reveals surprising binding mode

Area of Science:

• Biochemistry
• Medicinal Chemistry
• Structural Biology

Background:

• Thrombin is a key enzyme in blood coagulation.
• Inhibitors targeting thrombin are crucial for anticoagulant therapies.
• Understanding enzyme-inhibitor interactions guides drug design.

Purpose of the Study:

• To synthesize and evaluate novel thrombin inhibitors based on structural insights of the S1 pocket.
• To investigate the inhibitory activity of derivatives with varying side-chain sizes.
• To elucidate the binding mechanism of potent inhibitors.

Main Methods:

• Synthesis of Boc-D-trimethylsilylalanine-proline-boro-X pinanediol derivatives.
• Structural comparison of the S1 pocket in trypsin-like serine proteases.
• Enzyme inhibition assays to determine potency (nM range).
• X-ray crystallography to determine the inhibitor-thrombin complex structure.

Main Results:

• A series of novel thrombin inhibitors were synthesized.
• Compounds with side chains too large for the S1 pocket exhibited potent nanomolar inhibition.
• X-ray structure revealed a previously unrecognized binding mode for these inhibitors.

Conclusions:

• The study identified potent thrombin inhibitors with an unexpected binding mode.
• Structural flexibility or alternative interactions allow inhibition despite S1 pocket steric hindrance.
• These findings offer new strategies for designing effective anticoagulants.