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Target fishing for constituents from Ruta graveolens using a virtual parallel screening approach
Secondary plant metabolites are known to exert a multitude of biological effects. Finding the corresponding targets is however a demanding task. In this study we applied a virtual parallel screening approach  using Discovery Studio (Accelrys Inc., CA) to identify relevant targets for 16 secondary metabolites, which have been isolated and identified from the dichloromethane and methanol extracts of the aerial parts of the medicinal plant Ruta graveolens L.. 255 structural conformations of every isolate were calculated and screened against an extensive set of in-house generated pharmacophore models for the in silico prediction of putative biological targets, i.e. target fishing. Based on the predicted ligand-target interactions, we focused on three biological proteins, namely acetylcholinesterase (AChE), human rhinovirus (HRV) coat protein, and the cannabinoid receptor 2 (CB2). For a critical assessment of the applied parallel screening approach, virtual hits and non-hits were evaluated for their interaction with the respective biological targets. In case of AChE the highest scored virtual hit, arborinine, showed also the best in vitro inhibitory activity on AChE (IC50 34.7±7.1µM). Determination of the cytopathic inhibitory effect by HRV-2 infection  revealed 6,7,8-trimethoxy coumarine and arborinine as the most active antiviral constituents. Among them, only arborinine was virtually predicted. From all the molecules subjected to the parallel screening, one virtual hit for CB2 was identified, i.e. rutamarin. Interestingly, in the experimental studies only this compound showed a significant binding interaction in the radioligand displacement assay  with a Ki of 7.4±0.6µM.
To sum up, the parallel screening approach exemplified with constituents of R. graveolens on three different proteins showed to be a highly promising computer-assisted tool for rational target fishing in pharmacognostic research.
References: 1. Rollinger, J.M. et al. (2008). Virtual Screening for the Discovery of Bioactive Natural Products. In: Natural Compounds as Drugs, Vol. I; 212–49. 2. Schmidtke, M. et al. (2001)J Virolog Methods 95:133–43. 3. Raduner, S. et al. (2006)J Biol Chem 281:14192–6.