Possible Thrombus-clearing Mechanism and Modification Suggestion of β-sitosterol

Area of Science:

• Biochemistry
• Computational Biology
• Pharmacology

Background:

• Thrombin (THR) is a critical target for anticoagulant therapies.
• The precise mechanism by which β-sitosterol, a natural compound with antithrombotic properties, inhibits THR remains largely unknown.

Purpose of the Study:

• To elucidate the molecular recognition and inhibition mechanism of β-sitosterol on human thrombin.
• To provide insights for the rational design of novel allosteric THR inhibitors.

Main Methods:

• Integrated AI-driven structural alignment, molecular docking, and Molecular Dynamics (MD) simulations.
• Employed binding free energy calculations and Density Functional Theory (DFT) for mechanistic analysis.
• Designed and predicted the activity of novel sterol derivatives based on simulation findings.

Main Results:

• β-sitosterol binding is stabilized by hydrophobic and van der Waals interactions, causing active site closure and EF_loop conformational changes.
• These alterations effectively occlude the catalytic site, impairing thrombin's proteolytic activity.
• Designed sterol derivatives showed improved binding affinity, with compound d3 identified as a promising inhibitor with good ADMET properties.

Conclusions:

• This study reveals the atomic-level mechanism of β-sitosterol's inhibition of thrombin.
• The findings support the rational design of allosteric THR inhibitors, including novel sterol derivatives.
• Further in vitro and in vivo studies are recommended to validate the observed inhibitory activity.