Liu et al. discovered two potent IGF-1R kinase inhibitors via hierarchical strategy based virtual screening (pharmacophore screening and docking), which efficiently reduced the number of "nonhits" passed to docking stage and consequently reduced the computational cost [36].
An association of virtual screening, docking and a good rescoring procedure is a well known technique to discover and design new lead compounds in medicinal chemistry.
We identified a quinoxaline moiety as a new small-molecule inhibitor of the LRP5/6-sclerostin interaction through pharmacophore-based virtual screening, docking simulations, and in vitro assays.
In order to assess the performance of different fingerprint approaches (PADIF, IFP, TIFP), conventional ChemPLP scoring and a combination of PADIF and ChemPLP in virtual screening, docking experiments were performed for 39 datasets of the DUD [18], comprising targets from different, highly relevant protein classes.
For example, the same techniques were born in the last years, like virtual screening, docking as far as evolution of dynamic simulations, steered molecular dynamics (SMD) [ 2], or metadynamic studies.
Ajay et al. [82] used in silico assays, including pharmacophore mapping and 3D database searching, followed by SADMET-based virtual screening, docking analysis, and toxicity studies, and discovered 8 nontoxic PTPRF inhibitors.
Based on active site structural differences between LSS and human spermidine synthase (HSS), we screened a large dataset of compounds against modeled protein using Glide virtual screen docking and selected two best inhibitors based on their docking scores (− 10.04 and − 13.11 respectively) with LSS and having least/no binding with the human enzyme.
Docking virtual screening searches were carried out to screen a pre-filtered in-house database of 540,000 compounds with our published cell-based partition chemistry-space matrix calculation algorithm48, 66,67,68, in which the docking score was expressed in -log10(K d).
Such structural information would enhance the druggability value by facilitating a structure-based drug design strategy, including homology modeling, docking, virtual screening or pharmacophore-based screening [29], [30].
Such information could greatly facilitate a structure-based drug design, including homology modeling, docking, virtual screening or pharmacophore-based screening.
Unlike conventional virtual screening, ensemble docking is able to address the degree of freedom during molecular docking process and hence increase the chances of better hit for potential inhibitor.
