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Proven in vitro evolution of protease cathepsin E-inhibitors and -activators at pH 4.5 using a paired peptide method

Authors

  • Koichiro Kitamura,

    1. Janusys Corporation, #508, Saitama Industrial Technology Center, Kawaguchi, Saitama, Japan
    2. Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
    3. Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS), Saitama Small Enterprise Promotion Corporation, #552, Saitama Industrial Technology Center, Kawaguchi, Saitama, Japan
    4. City Area Program Saitama Metropolitan Area, Saitama small and medium Enterprises Development Corporation, Saitama City, Saitama, Japan
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  • Masayuki Komatsu,

    1. Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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  • Madhu Biyani,

    1. Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
    2. City Area Program Saitama Metropolitan Area, Saitama small and medium Enterprises Development Corporation, Saitama City, Saitama, Japan
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  • Masae Futakami,

    1. Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
    2. City Area Program Saitama Metropolitan Area, Saitama small and medium Enterprises Development Corporation, Saitama City, Saitama, Japan
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  • Tomoyo Kawakubo,

    1. Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS), Saitama Small Enterprise Promotion Corporation, #552, Saitama Industrial Technology Center, Kawaguchi, Saitama, Japan
    2. City Area Program Saitama Metropolitan Area, Saitama small and medium Enterprises Development Corporation, Saitama City, Saitama, Japan
    3. Proteolysis Research Laboratory, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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  • Kenji Yamamoto,

    1. Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS), Saitama Small Enterprise Promotion Corporation, #552, Saitama Industrial Technology Center, Kawaguchi, Saitama, Japan
    2. City Area Program Saitama Metropolitan Area, Saitama small and medium Enterprises Development Corporation, Saitama City, Saitama, Japan
    3. Proteolysis Research Laboratory, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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  • Koichi Nishigaki

    Corresponding author
    1. Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS), Saitama Small Enterprise Promotion Corporation, #552, Saitama Industrial Technology Center, Kawaguchi, Saitama, Japan
    2. City Area Program Saitama Metropolitan Area, Saitama small and medium Enterprises Development Corporation, Saitama City, Saitama, Japan
    • Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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Koichi Nishigaki, Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan. E-mail: koichi@fms.saitama-u.ac.jp

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. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.

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