Using Molecular Docking, 3D-QSAR, and Cluster Analysis for Screening Structurally Diverse Data Sets of Pharmacological Interest

In this study, we propose a drug design approach which includes docking, molecular fingerprints based cluster analysis, and ‘induced’ descriptors based receptor-dependent 3D-QSAR. The method was shown to be very useful for screening and modeling structurally diverse data sets of pharmacological interest. Different from other receptor-dependent 3D-QSAR, no ambiguous alignments are required for the construction of the models, and the computational cost is relatively lower. Moreover, ‘induced’ descriptors were shown to be very powerful in “capturing” ligand−receptor intermolecular interactions. The methodology was validated for eight data sets sampled from the literature and from public databases: human sex hormone-binding globulin, human corticosteroid-binding globulin, anthrax lethal factor, HIV-1 reverse transcriptase, neuraminidase A, thrombin, trypsin, and Pneumocystis carinii dihydrofolate reductase data sets. The resulting models were interpretable; the constructed QSAR equations have high statistical significance and predictive strength; and the drug design solutions were shown to be useful for guiding ligand modification for the development of new inhibitors for a broad range of molecular targets.