Bound Water Can Change the Ranking of Natural Product Ligands in Structure-Based Screening, Free-Energy Estimation, and Mechanistic Binding Analysis

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Water molecules buried or partially confined at protein–ligand interfaces are often treated as structural details to be retained, deleted, or optimized during receptor preparation. That simplification is consequential when alternative water states change hydrogen-bond topology, ligand desolvation, pocket reorganization, or the convergence of binding free-energy calculations. This computational pharmacology perspective examines how structural waters, hydration sites, water-displacement states, and water-mediated interaction networks can influence the prioritization and mechanistic interpretation of natural-product ligands. The analysis distinguishes experimentally observed waters from ensemble hydration sites and thermodynamic water states, then connects those distinctions to docking, scoring, free-energy estimation, and ligand-ranking uncertainty. Natural products are not assumed to be intrinsically more water dependent than synthetic ligands; rather, selected natural-product and natural-product-like chemotypes may create difficult cases because dense polar functionality, stereochemical constraint, macrocyclic architecture, and solvent-responsive conformations can support competing direct and water-mediated binding microstates. The principal contribution is a proposed water-aware prioritization perspective in which robustness across defensible hydration hypotheses becomes an additional criterion for interpreting ligand rank. This approach does not presume that explicit water universally improves prediction or that water-state changes always reverse ranking. Its value instead lies in identifying cases in which hydration assumptions become decision-relevant and warrant higher-resolution sampling or experimental interrogation. The perspective is bounded by force-field error, incomplete protein and ligand-state sampling, uncertainty in experimental water assignment, target dependence, and the absence of prospective validation across broad natural-product chemical space.