16 research outputs found
Assessing the stability of free-energy perturbation calculations by performing variations in the method
Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study
Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2
Ranking docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenge 2
Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model
Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2
Insights into mechanism of anticancer activity of pentacyclic oxindole alkaloids of Uncaria tomentosa by means of a computational reverse virtual screening and molecular docking approach
Alkaloid-rich extract from Uncaria tomentosa (eng. Cat’s claw) has been reported to cause apoptosis in vitro in cancer lines. Oxindole pentacyclic alkaloids of the plant are responsible for this effect, yet their biological mechanism of action is not fully understood. In this work the set of these alkaloids underwent an extensive theoretical study with reverse virtual screening and molecular docking methods implemented in AutoDock, AutoDock Vina and Molegro Virtual Docker. The obtained results from these computational methods indicate that inhibition of dihydrofolate reductase and MDM2 may be responsible for the biological activity of the alkaloids. The docking results also show that alkaloids can interact with Dvl-2, Akt-2 and leukotriene A4 hydrolase. The reverse virtual screening and molecular docking are valuable tools to aid identification of protein targets for bioactive hit molecules and could guide the design of in-depth biochemical activity tests and utilization of these alkaloids in anticancer drug development.Peer reviewe