Abstract
Hydration is one of the key players in the protein–ligand binding process. It not only influences the binding process per se, but also the drug’s absorption, distribution, metabolism, and excretion properties. To gain insights into the hydration of aromatic cores, the solvation thermodynamics of 40 aromatic mono- and bicyclic systems, frequently occurring in medicinal chemistry, are investigated. Thermodynamics is analyzed with two different methods: grid inhomogeneous solvation theory (GIST) and thermodynamic integration (TI). Our results agree well with previously published experimental and computational solvation free energies. The influence of adding heteroatoms to aromatic systems and how the position of these heteroatoms impacts the compound’s interactions with water is studied. The solvation free energies of these heteroaromatics are highly correlated to their gas phase interaction energies with benzene: compounds showing a high interaction energy also have a high solvation free energy value. Therefore, replacing a compound with one having a higher gas phase interaction energy might not result in the expected improvement in affinity. The desolvation costs counteract the higher stacking interactions, hence weakening or even inverting the expected gain in binding free energy.
Highlights
Stacking interactions between π-systems play a key role in a variety of materials and applications in chemistry, physics, and biology
In the case of grid inhomogeneous solvation theory (GIST), values for the solvation free energy, enthalpy, and entropy were obtained by integrating over all grid points within 5 Å of the solute
We found that the correlation of thermodynamic integration (TI) and GIST is excellent; both our results agree well with previously published experimental and computational data
Summary
Stacking interactions between π-systems play a key role in a variety of materials and applications in chemistry, physics, and biology. These interactions effect polymers, organic synthesis, liquid crystals, DNA, RNA, and protein structures, as well as protein−ligand interactions. They include π−π,1 cation−π,2,3 halogen−π,4,5 and hydrogen bonding interactions via heteroatoms.[6]. Most theoretical studies are done in the gas phase, completely neglecting the solvent and its effects.[7−11] Studies including the solvation of aromatic compounds are sparse. The group of Kim studied the solvation thermodynamics of two stacked benzene rings thoroughly, using a quantum/molecular mechanic (QM/MM) approach.[12]
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