Parametrization strategy for the MolFESD concept: quantitative surface representation of local hydrophobicity

Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient

The use of a recently proposed hydrophobic similarity index for the alignment of molecules and the prediction of their differences in biological activity is described. The hydrophobic similarity index exploits atomic contributions to the octanol/water transfer free energy, which are evaluated by means of the fractional partitioning scheme developed within the framework of the Miertus-Scrocco-Tomasi continuum model. Those contributions are used to define global and local measures of hydrophobic similarity. The suitability of this computational strategy is examined for two series of compounds (ACAT inhibitors and 5-HT3 receptor agonists), which are aligned to maximize the global hydrophobic similarity using a Monte Carlo-simulated protocol. Indeed, the concept of local hydrophobic similarity is used to explore structure-activity relationships in a series of COX-2 inhibitors. Inspection of the 3D distribution of hydrophobic/hydrophilic contributions in the aligned molecules is valuable to identify regions of very similar hydrophobicity, which can define pharmacophoric recognition patterns. Moreover, low similar regions permit to identify structural elements that modulate the differences in activity between molecules. Finally, the quantitative relationships found between the pharmacological activity and the hydrophobic similarity index points out that not only the global hydrophobicity, but its 3D distribution, is important to gain insight into the activity of molecules.

Surface-Integral QSPR Models: Local Energy Properties

Surface-integral models based on AM1 semiempirical molecular orbital calculations are presented for the free energies of solvation in water, n-octanol, and chloroform and for the enthalpy of solvation in water. A parametrized function of four local properties calculated at the isodensity surface (the molecular electrostatic potential, local ionization energy, electron affinity, and polarizability) is integrated over the triangulated surface area to obtain the target quantity. The resulting models give results only slightly less accurate than those reported for parametrized generalized Born/polar surface area models despite relying only on gas-phase calculations. The water and octanol free-energy models were validated by calculating the water-octanol partition coefficient for a test set of organic compounds with moderate success. The models lead to a local solvation energy, which can be projected onto the molecular isodensity surface and provides insight into "hot" areas for solvation in water or the other solvents.

QSAR and QSPR based solely on surface properties?

The use of descriptors based on local properties calculated at the molecular surface for QSPR models is discussed. It is suggested that descriptors should be related to the physical theory of intermolecular interactions and the relationship between established surface-based descriptors and the fundamental types of intermolecular interaction is discussed. Descriptors based on local properties that do not encode the chemical constitution of the molecule directly are likely to provide less local QSPR models and favor scaffold hopping. The major disadvantage for surface-based descriptors is that they are difficult to interpret in the sense of relating predictions to the chemical composition of the molecule. This disadvantage must be alleviated by suitable model-interrogation techniques.