BackgroundLigand-based in silico target fishing can be used to identify the potential interacting target of bioactive ligands, which is useful for understanding the polypharmacology and safety profile of existing drugs. The underlying principle of the approach is that known bioactive ligands can be used as reference to predict the targets for a new compound.ResultsWe tested a pipeline enabling large-scale target fishing and drug repositioning, based on simple fingerprint similarity rankings with data fusion. A large library containing 533 drug relevant targets with 179,807 active ligands was compiled, where each target was defined by its ligand set. For a given query molecule, its target profile is generated by similarity searching against the ligand sets assigned to each target, for which individual searches utilizing multiple reference structures are then fused into a single ranking list representing the potential target interaction profile of the query compound. The proposed approach was validated by 10-fold cross validation and two external tests using data from DrugBank and Therapeutic Target Database (TTD). The use of the approach was further demonstrated with some examples concerning the drug repositioning and drug side-effects prediction. The promising results suggest that the proposed method is useful for not only finding promiscuous drugs for their new usages, but also predicting some important toxic liabilities.ConclusionsWith the rapid increasing volume and diversity of data concerning drug related targets and their ligands, the simple ligand-based target fishing approach would play an important role in assisting future drug design and discovery.
One of the key shortcomings in the field of nanotechnology risk assessment is the lack of techniques capable of source tracing of nanoparticles (NPs). Silica is the most-produced engineered nanomaterial and also widely present in the natural environment in diverse forms. Here we show that inherent isotopic fingerprints offer a feasible approach to distinguish the sources of silica nanoparticles (SiO
2
NPs). We find that engineered SiO
2
NPs have distinct Si–O two-dimensional (2D) isotopic fingerprints from naturally occurring SiO
2
NPs, due probably to the Si and O isotope fractionation and use of isotopically different materials during the manufacturing process of engineered SiO
2
NPs. A machine learning model is developed to classify the engineered and natural SiO
2
NPs with a discrimination accuracy of 93.3%. Furthermore, the Si–O isotopic fingerprints are even able to partly identify the synthetic methods and manufacturers of engineered SiO
2
NPs.
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