On the Role of Solvation in Ligand Binding: Structural and Thermodynamic Studies

<p>Water is known to be the matrix of life. Liquid water, which is present in every living organism, is indispensable for all biological processes. Doubtlessly, water molecules play a critical role in ligand binding. In spite of its fundamental thermodynamic impact, solvent energetics is often bypassed in virtual screening. On the one hand, the determination of water energetics is generally hampered by the cooperative nature of these interactions. On the other hand, accounting for the correct energetic cost for water displacement by the ligand is thought to be one of the factors that limits the accuracy of docking. In addition, despite this critical role of water, experimental techniques that specifically provide information about solvation energetics are very limited. The first part of this dissertation discusses structural evidence for cases where water can play a favorable role in ligand binding. In the second part, the fact that the solvent can compete with ligand binding is discussed. Accounting for such effects allowed the development of strategies that enabled the determination of ligand affinity based on structural data. Finally, we developed a density-based solvation method that deduces solvent energetics directly from crystallographic electron density maps. To illustrate its feasibility, the method was applied to idealized electron density maps that were calculated from Molecular Dynamics trajectories. Unlike idealized electron density maps computed from atomic coordinates, the application of our solvation method to experimental density maps faced several challenges. These challenges were addressed, allowing the method to become applicable to experimental electron density maps.</p>

Name thesis:degree_name

Doctor of Philosophy (PhD)

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Pharmaceutical Sciences

Year dc:date.available

2025

Author dc:creator

• Alaidi, Osama Abdulla

Contributors dc:contributor

• Kirk Hevener

• BPTF
• Electron Density Maps
• Ligand Binding
• Solvation
• Structural Biology
• X-ray Crystallography
• Biophysics
• Chemistry

Repository record dc:identifier

https://dc.uthsc.edu/dissertations/716

OAI identifier oai:identifier

oai:dc.uthsc.edu:dissertations-1716