Compounds binding to the S2-S3 pockets of thrombin

Area of Science:

• Medicinal Chemistry
• Biochemistry
• Structural Biology

Background:

• Thrombin is a key enzyme in blood coagulation.
• Targeting thrombin's S2-S3 pockets offers a strategy for inhibitor design.
• Understanding ligand interactions with serine protease pockets is crucial.

Purpose of the Study:

• To design and synthesize novel thrombin inhibitors targeting the S2-S3 pockets.
• To investigate the impact of P1 substituents and hydrogen bonding on binding affinity.
• To elucidate the binding mode and guide future drug discovery efforts.

Main Methods:

• Synthesis of diverse compound libraries.
• Surface Plasmon Resonance (SPR) biosensor technology for binding constant determination.
• Enzyme assays for validating binding affinities.
• X-ray crystallography for structural analysis.
• Quantitative Structure-Activity Relationship (QSAR) modeling.

Main Results:

• Compounds with an amino group showed a 100-1000 fold increase in binding affinity due to hydrogen bonding with Gly216.
• Increased ligand efficiency was achieved through hydrophobic interactions in the P1 pocket.
• X-ray analysis confirmed the predicted binding mode, including hydrogen bonds and a bound water molecule.
• QSAR models highlighted the importance of hydrogen bonding and lipophilicity for binding constants.

Conclusions:

• Hydrogen bonding interactions, particularly with Gly216, significantly enhance thrombin inhibitor potency.
• Optimizing hydrophobic interactions in the P1 pocket improves ligand efficiency.
• Structural and QSAR data provide a foundation for designing targeted compound libraries for shallow protease pockets.