title: Proven in vitro evolution of protease cathepsin E-inhibitors and -activators at pH 4.5 using a paired peptide method.
abstract: Improving a particular function of molecules is often more difficult than identifying such molecules ab initio. Here, a method to acquire higher affinity and/or more functional peptides was developed as a progressive library selection method. The primary library selection products were utilized to build a secondary library composed of blocks of 4 amino acids, of which selection led to peptides with increased activity. These peptides were further converted to randomly generate paired peptides. Cathepsin E-inhibitors thus obtained exhibited the highest activities and affinities (pM order). This was also the case with cathepsin E-activating peptides, proving the methodological effectiveness. The primary, secondary, and tertiary library selections can be regarded as module-finding, module-shuffling, and module-pairing, respectively, which resembles the progression of the natural evolution of proteins. The mode of peptide binding to their target proteins is discussed in analogy to antibodies and epitopes of an antigen.
authors.affiliation: Janusys Corporation, #508, Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama, 333-0844, Japan; Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama, 338-8570, Japan; Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS), Saitama Small Enterprise Promotion Corporation, #552, Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama, 333-0844, Japan; City Area Program Saitama Metropolitan Area, Saitama small and medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-ku, Saitama City, Saitama, 338-0001, Japan.
authors.forename: Koichiro
authors.initials: K
authors.lastname: Kitamura
authors.forename: Masayuki
authors.initials: M
authors.lastname: Komatsu
authors.forename: Madhu
authors.initials: M
authors.lastname: Biyani
authors.forename: Masae
authors.initials: M
authors.lastname: Futakami
authors.forename: Tomoyo
authors.initials: T
authors.lastname: Kawakubo
authors.forename: Kenji
authors.initials: K
authors.lastname: Yamamoto
authors.forename: Koichi
authors.initials: K
authors.lastname: Nishigaki
mesh_terms: D000595:Amino Acid Sequence; D052158:Aptamers, Peptide / Q000737:chemistry*; D020059:Cathepsin E / Q000037:antagonists & inhibitors*; D019020:Directed Molecular Evolution; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D019151:Peptide Library; D011480:Protease Inhibitors / Q000737:chemistry*; D011485:Protein Binding
chemical_list: D052158:Aptamers, Peptide; D019151:Peptide Library; D011480:Protease Inhibitors; D020059:Cathepsin E
keywords: cDNA display; cathepsin E; in vitro evolution; module-shuffling; paired peptides