Synthesis of Random Peptide Libraries Synthesis of random peptide libraries is accomplished by standard solid- phase peptide synthetic methods. 6-9 FIuorenylmethyloxycarbonyl (Fmoc)

The application of combinatorial technologies has become a significant trend in pharmaceutical research. The combinatorial discovery process consists of two parts: the generation of collections of molecular diversity, known as libraries, by systematic connection of different building blocks, and screening of such libraries with target molecules to identify novel compounds that interact with them. 1-3 Thus, the combinatorial approach requires not only the design and construction of libraries of chemical diversity, but also the development of novel screening and assay methodologies for library evolution. Using a split synthesis method, peptide bead libraries can be synthesized such that each bead contains only one peptide species: the "one bead-one peptide concept. ''4-6 The lead discovery approach based on such libraries is known as the "Selectide process. ''3-6 This chapter describes three different protocols that have been successfully applied for the screening of such "one bead-one peptide" libraries: (i) to identify substrates for two protein kinases, (ii) to find specific peptide sequences that bind small organic molecules, and (iii) to optimize the biological potency of a known human thrombin inhibitor. According to the characteristics and objectives of each system, we used different approaches including in situ autoradiography, direct binding of organic dye, and enzyme-linked binding assay.