After over a decade of studies on aspartic protease inhibitors and water-soluble prodrugs, we have been developing a novel method, since 2003, called 'O-acyl isopeptide method', for the synthesis of peptides containing difficult sequences. With our recent discoveries of 'O-acyl isodipeptide unit' and the 'racemization-free segment condensation method', this method has further evolved as a general synthetic method for peptides. Moreover, 'Click Peptide', which could be a powerful tool for identifying the pathological functions of amyloid beta peptides in Alzheimer's disease, represents a valuable use of the isopeptide method in Chemical Biology-oriented research.