A systems guide to chemical-biological interactions

Tudor Oprea (with Jarret Hines-Kay and Gergely Zahoranszky-Kohalmi) University of New Mexico

Small molecule perturbation of biological responses represents one of the cornerstones of biochemistry, pharmacology, and chemical biology. Significant resources, such as comprehensive bioactivity databases, can now be used for knowledge mining in drug discovery and repurposing. The ‘CARLSBAD’ platform provides access to the scientific community to a large-scale database confederating and consolidating many bioactivity databases, e.g., IUPHAR and PDSP (pharmacology), WOMBAT and CheMBL (biochemistry and medicinal chemistry), and PubChem (chemical biology). This platform can be queried via the web interface ‘SNAKE’, which supports target-based, ligand-based, and chemical pattern (CP) -based exploration of chemico-biological data. The results obtained via SNAKE are provided in network format, which can be directly visualized in Cytoscape. This approach enables network-inference analytics for bioactivity data, using the CARLSBAD cytoscape plugin (based on ChemAxon software). This plugin integrates a number of algorithms from chemoinformatics and complex network theory, and offers a systems view of complex ligand-protein interactions, which can be used to seek new drug targets or new lead compounds. Several examples based on this approach will be highlighted.

NB: During the tutorial, we would like attendees to work through some hands-on exercises using our software platform. This platform is the focus of the tutorial and consists of several components. For this reason we think it would be best if you could come to the tutorial with the proper software environment already set up. To this end we have compiled a manual, which provides all the information to make the necessary preparations for your computer. Please feel free to contact us if you have any questions about setting up the software platform.