To understand the energetics of the interaction between protein and DNA we analyzed 39 crystallographically characterized complexes with the HINT (Hydropathic INTeractions) computational model. HINT is an empirical free energy force field based on solvent partitioning of small molecules between water and 1-octanol. Our previous studies on protein-ligand complexes demonstrated that free energy predictions were significantly improved by taking into account the energetic contribution of water molecules that form at least one hydrogen bond with each interacting species. An initial correlation between the calculated HINT scores and the experimentally determined binding free energies in the protein-DNA system exhibited a relatively poor r² of 0.21 and standard error of ± 1.71 kcal mol^-1. However, the inclusion of 261 waters that bridge protein and DNA improved the HINT score-free energy correlation to an r² of 0.56 and standard error of ± 1.28 kcal mol^-1. Analysis of the water role and energy contributions indicate that 46% of the bridging waters act as linkers between amino acids and nucleotide bases at the protein-DNA interface, while the remaining 54% are largely involved in screening unfavorable electrostatic contacts. This study quantifies the key energetic role of bridging waters in protein-DNA associations. In addition, the relevant role of hydrophobic interactions and entropy in driving protein-DNA association is indicated by analyses of interaction character showing that, together, the favorable polar and unfavorable polar/hydrophobic-polar interactions (i.e., desolvation) mostly cancel.

Estrogen Receptors (ERs) are ligand-dependent intracellular transcriptional factors involved in many diseases. ERs mediate many of the effects of estrogens, but also exogenous compounds are able to interfere with ER, disrupting endocrine signaling. Among these xenobiotics, compounds present in food and feed make ERs a relevant target in the context of dietary modulation of health. In this sense, urolithins, gut microbiota derived metabolites of plant polyphenolic ellagitannins, may represent good candidates to act as phytoestrogens that are able to modulate the activity of ERs. An in silico method to qualitatively evaluate the potential xenoestrogenic agonistic behavior of ellagitannin-derived metabolites is proposed. The “full-dry” in silico approach involved structure based virtual screening (SBVS), docking simulations and re-scoring procedures. Results provided valuable insights about the phase II conjugations (glucuronidation, sulfation, and methylation, occurring in vivo) affecting the estrogenicity of these compounds on α- and β-ER isoforms. Hydroxylation patterns also revealed a significant role in the agonistic behavior of urolithin derivatives. On the whole, ellagitannin-derived metabolites exerted different predicted xenoestrogenic activity depending on chemical structures, and the applied in silico approach may represent a successful and easy choice to analyze enormous datasets of food-related compounds in order to understand their potential biological features.