SwissTargetPrediction: a web server for target prediction of bioactive small molecules

Abstract

Bioactive small molecules, such as drugs or metabolites, bind to proteins or other macro-molecular targets to modulate their activity, which in turn results in the observed phenotypic effects. For this reason, mapping the targets of bioactive small molecules is a key step toward unraveling the molecular mechanisms underlying their bioactivity and predicting potential side effects or cross-reactivity. Recently, large datasets of protein–small molecule interactions have become available, providing a unique source of information for the development of knowledge-based approaches to computationally identify new targets for uncharacterized molecules or secondary targets for known molecules. Here, we introduce SwissTargetPrediction, a web server to accurately predict the targets of bioactive molecules based on a combination of 2D and 3D similarity measures with known ligands. Predictions can be carried out in five different organisms, and mapping predictions by homology within and between different species is enabled for close paralogs and orthologs. SwissTargetPrediction is accessible free of charge and without login requirement at http://www.swisstargetprediction.ch.

Investigation of the anti-aging properties of allicin from <i>Allium sativum</i> L bulb extracts by a reverse docking approach

“…The specific protein target of A. sativum ligands was predicted using Swiss Target Prediction (http://swisstargetprediction.ch) [19]. Molecular docking of allicin, epigallocatechin and pedunculagin analysis was done using Pyrx 0.8.…”

Piper longum: A review of its phytochemicals and their network pharmacological evaluation

“…The compiled dataset was filtered to remove duplicate entries. Human proteins targeted by the phytochemicals were predicted from STITCH 5.0 (Search Tool for Interactions of Chemicals and proteins) (Szklarczyk et al, 2015), BindingDB (Liu et al, 2006), SwissTargetPrediction (Gfeller et al, 2014) and PCIDB.…”

Crystal structure, Hirshfeld analysis and molecular docking with the vascular endothelial growth factor receptor-2 of (3Z)-5-fluoro-3-(hydroxyimino)indolin-2-one

“…The calculated parameters were: heat of formation = À49.353 kJ mol À1 , gradient normal = 0.90997, HOMO = À9.265 eV, LUMO = À1.337 eV and energy gap = 7.928 eV (Macrae et al, 2008;Stewart, 2013Stewart, , 2016. The biological target prediction for the title compound was calculated with the SwissTargetPrediction webserver based on the bioisosteric similarity to the isatin entity (Gfeller et al, 2013(Gfeller et al, , 2014. As result of this screening, the title compound showed a promising theoretical structure-activity relationship to kinase proteins sites: 'Frequency Target Class' for kinases amounts to 33% [see the 'SwissTargetPrediction report (5-fluoroisatin-3-oxime)' in the Supporting information].…”