In this article, a technique for accurate direct measurement of protein-to-protein interactions before and after the introduction of a drug candidate is developed using atomic force microscopy (AFM). The method is applied to known immunosuppressant drug candidate Echinacea purpurea derived cynarin. T-cell/CD28 is on-chip immobilized and B-cell/CD80 is immobilized on an AFM tip. The difference in unbinding force between these two proteins before and after the introduction of cynarin is measured. The method is described in detail including determination of the loading rates, maximum probability of bindings, and average unbinding forces. At an AFM loading rate of 1.44 x 104?pN/s, binding events were largely reduced from 61?+/- 5% to 47?+/-?6% after cynarin introduction. Similarly, maximum probability of bindings reduced from 70% to 35% with a blocking effect of about 35% for a fixed contact time of 0.5?s or greater. Furthermore, average unbinding forces were reduced from 61.4 to 38.9?pN with a blocking effect of similar to 37% as compared with similar to 9% by SPR. AFM, which can provide accurate quantitative measures, is shown to be a good method for drug screening. The method could be applied to a wider variety of drug candidates with advances in bio-chip technology and a more comprehensive AFM database of protein-to-protein interactions. Biotechnol. Bioeng. 2012; 109: 24602467. (c) 2012 Wiley Periodicals, Inc.