Date of Award
2025
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Program
Pharmaceutical Sciences
Track
Pharmacometrics
Research Advisor
Kirk Hevener
Committee
David Nelson; Glen Palmer; Kirk Hevener; Mohamed Laradji; Seetharaman Jayaraman
Keywords
BPTF, Electron Density Maps, Ligand Binding, Solvation, Structural Biology, X-ray Crystallography
Abstract
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.
ORCID
https://orcid.org/0000-0002-1292-6789
DOI
10.21007/etd.cghs.2025.0696
Recommended Citation
Alaidi, Osama Abdulla (https://orcid.org/0000-0002-1292-6789), "On the Role of Solvation in Ligand Binding: Structural and Thermodynamic Studies" (2025). Theses and Dissertations (ETD). Paper 716. http://dx.doi.org/10.21007/etd.cghs.2025.0696.
https://dc.uthsc.edu/dissertations/716