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Since the development of structure–activity relationships about 50 years ago, 3D‐QSAR methods belong to the most refined ligand‐based in silico techniques for prediction of biological data using physicochemical molecular fields. In this scenario, this study reports the development and validation of quantum mechanical (QM)‐based hydrophobic descriptors derived from the parametrized MST continuum solvation model to be used in 3D‐QSAR studies within the framework of the Hydrophobic Pharmacophore (HyPhar) method. To this end, five sets of compounds reported in the literature (dopamine D2/D4 antagonists, antifungal 2‐aryl‐4‐chromanones, and inhibitors of GSK‐3, cruzain and thermolysin) have been revisited. The results derived from the QM/MST‐based hydrophobic descriptors have been compared with previous CoMFA and CoMSIA studies, and examined in light of the available X‐ray …