Fragment Binding Can Be Either More Enthalpy-Driven or Entropy-Driven: Crystal Structures and Residual Hydration...

Area of Science:

• Medicinal Chemistry
• Structural Biology
• Drug Discovery

Background:

• Fragment-based drug discovery (FBDD) relies on identifying small molecules that bind to biological targets.
• Thermodynamic signatures are crucial for selecting fragments during lead optimization to predict binding affinity.
• Enthalpic advantage in early-stage fragments is often preferred due to inevitable entropic penalties in later optimization.

Purpose of the Study:

• To determine the thermodynamic profiles of six fragments binding to the S1 pocket of thrombin.
• To correlate fragment binding modes and thermodynamic properties with binding potency.
• To guide fragment selection for further lead optimization in drug development.

Main Methods:

• High-resolution crystal structures of six fragments bound to the thrombin S1 pocket were determined.
• Thermodynamic analysis of fragment binding was performed.
• Binding modes and interactions, including solvation networks, were analyzed.

Main Results:

• The most potent fragments (amidine scaffold) were not the most enthalpic; a chloro-thiophene fragment showed higher enthalpy.
• Two similar chloro-aromatic fragments exhibited a large potency difference (430 μM vs 10 mM) due to distinct binding modes and water networks.
• The more potent chloro-aromatic fragment engaged a water molecule and Glu192, effectively capping the S1 pocket, correlating with optimal solvation patterns and higher potency.

Conclusions:

• Fragment potency is strongly influenced by specific binding interactions and the recruitment of water molecules, not solely by enthalpy.
• Optimized solvation patterns and interactions with key residues like Glu192 are critical for achieving high fragment potency.
• Thermodynamic and structural analysis provides essential insights for rational fragment selection in lead optimization.