The effect of various natural products and chemical compounds to their corresponding molecular target is often unidentified. Drugs are effective by binding to a molecule (the target) and inhibiting its function. In order to perform an efficient target-oriented drug discovery, target and related tests are needed. These tests are mostly based on a binding or catalytic function, which are usually visualized by optical methods. Subsequently, the cell- or enzyme-based drug tests can be done. In many cases, these tests are complex, expensive and time-consuming. To optimize these obstacles, a highly miniaturized microarray-based test for proteins has been developed which can be carried out with very small amounts of material. Purified proteins are the target of the active compounds, while the binding property of the targets for the ligand and possible drugs and their optimized derivatives are tested. Targets of different proteomes such as heat shock proteins 90 (Hsp90) and Hsp70, a cellular stressed or pathogenic, are studied with regard to drug susceptibility or diagnostic potential. Fluorescent ATP was used to visualize binding of the natural ligand and competition by potential drugs. It could be shown that the position of the fluorescent marker on the ATP influences the binding to the heat shock proteins Hsp90 and Hsp70 differently. The influence of an in-house drug library (~150 inhibitors) was investigated in the competitive assay with geldanamycin (Gda) as a lead structure for the ATP binding pocket on various heat shock proteins 90 (Hsp90). It was possible to identify Gda derivatives that bind very affine on human Hsp90 with Kd in the nanomolar range while exhibiting lower affinities for Hsp90 from Leishmania braziliensis. Compounds determined by microarray techniques were further confirmed by ITC and cell-based assays. Furthermore, the use of full-length Hsps in microarray-based assay made it possible to measure the interaction of L1CAM, a cell-cell adhesion protein with various proteins such as Hsp90, Hsp70, L1CAM and CsgA (Curli). In addition to the ability of microarray-based assays in testing the protein-ligand interactions, it has been also documented that it is possible to determine protein-protein interaction by this technique.