A streamlined computer aided drug design protocol has been developed in the Xu lab to screen an large in-house chemical database of over 1 million commercially available compounds. The screening protocol consists of a two-step filtering process based on 3D shape and electrostatic potential matching. The selected compounds are docked the targeted protein using AutoDock Vina and rescored with AutoDock 4. These compounds are ranked by their predicted binding free energies and the top hits are purchased and tested using in vitro biological assays. This highly efficient and accurate computational protocol has been applied in the ongoing drug design projects in collaboration with multiple experimental labs in the Chemistry and Biology departments, including anti-parasite/bacterial drug design (Cornell lab), anti-bacterial quorum sensing drug design (Raj lab), anti-cancer drug design (Jorcyk lab) and carbonyl reductase cardiotoxicity drug design (Charlier lab). It is anticipated these collaborative projects will yield novel therapeutics against a broad range of diseases.
Available at: http://works.bepress.com/cheryl_jorcyk/36/