A new rapid compound screening approach for topoisomerase I binding activity is presented. DNA topoisomerase I is used as a target protein to capture binding compounds from a mixture of combinatorial compounds by bioaffinity ultrafiltration. Using high-performance liquid chromatography combined with electrospray ionization mass spectrometry, small-molecule active compounds were identified. We also have successfully applied this method to identifying compounds from cells grown in culture. (C) 2004 Elsevier Inc. All rights reserved.