Descriptor GRID water probe

Fig. 3. Correlation of VolSurf descriptors with human intestinal absorption using multivariate statistics (PLS) based on 20 drug molecules as reported by Cuba et al. (2000). The PLS plot (ul versus tl) and the corresponding PLS coefficient plot is shown. Different interaction pattern with the GRID water probe are displayed for the orally available nordiazepam (left) versus the large area for the non-available...

Fig. 2. Computation of Volsurf descriptors (Cruciani et al. 2000a) derived from GRID molecular interaction fields. For any molecule, interactions with GRID water and dry probes at different energy levels are used for contouring. Those levels serve to compute vectors of 72 volume, size, and surface related descriptors.

Solubility is a key property in the distribution of the compound from the gastrointestinal tract to the blood. There have been several modeling efforts to predict the solubility, based on different type of descriptors. The intrinsic solubility (thermodynamic solubility of the neutral species) for a set of 1028 compounds has been modeled using the VolSurf descriptors based on GRID-MIFs (Fig. 10.9(a)) and PLS multivariate analysis [20]. The interpretation of the model can be based on the PLS coefficients the ratio of the surface that has an attractive interaction with the water probe contributes positively to the solubility, while the hydrophobic interactions and log P have a negative contribution. 

Fig. 14.5 Computation of VolSurf descriptors [155, 156] derived from GRID molecular interaction fields. Interactions of the example molecule with a water and dry probe at different contour levels are used to compute a vector of 72 volume-, size- and surface-based descriptors.

The set of 51 benzamidine-based thrombin inhibitors was taken from the study of Sugano et al. (2000). Experimental rat everted sac permeabilities were expressed as log(ES A) values.2 The experimental permeability in this assay is expressed as ratio of outer (mucosal side) concentration of the drug and inner (serosal side) concentration after 1 h incubation of the everted sac of rat small intestine. All molecules were treated in their neutral form and converted into their 3D structures using CORINA (Sadowski et al. 1992). From GRID molecular interaction fields for water, dry, and carbonyl oxygen probes, a set of 72 VolSurf descriptors (Cruciani et al. 2000) was computed and analysed as described above. 

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