Figure 1. Flow chart of virtual and experimental screening strategy for discovering EBNA1 inhibitors.

The EBNA1/DNA crystal structure was computationally fitted into a 6 Å grid containing every residue of the EBNA1 DNA-binding pocket was used to dock a library of compounds from the SPECS database. Compounds were preselected for solubility in an aqueous solution using a log S value of greater than −4. A database of ∼90,000 small-molecule compounds were then analyzed by one primary docking programs and three score functions to calculate the free energy of binding. 5000 candidates were then re-examined using Xscore, Slide, and AutoDock programs to select 30 top candidates. The top 30 compounds from 15 manually classified groups were selected for experimental DNA binding and cell-based bioassays.