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O-フタルアルデヒド基を用いたペプチドの高効率マクロ環化とその応用

Research Project

Project/Area Number 22KF0114
Project/Area Number (Other) 22F22334 (2022)
Research Category

Grant-in-Aid for JSPS Fellows

Allocation TypeMulti-year Fund (2023)
Single-year Grants (2022)
Section外国
Review Section Basic Section 37010:Bio-related chemistry
Research InstitutionThe University of Tokyo

Principal Investigator

菅 裕明  東京大学, 大学院理学系研究科(理学部), 教授 (00361668)

Co-Investigator(Kenkyū-buntansha) ZHANG YUE  東京大学, 大学院理学系研究科(理学部), 外国人特別研究員
Project Period (FY) 2023-03-08 – 2025-03-31
Project Status Granted (Fiscal Year 2023)
Budget Amount *help
¥2,200,000 (Direct Cost: ¥2,200,000)
Fiscal Year 2024: ¥500,000 (Direct Cost: ¥500,000)
Fiscal Year 2023: ¥1,100,000 (Direct Cost: ¥1,100,000)
Fiscal Year 2022: ¥600,000 (Direct Cost: ¥600,000)
KeywordsRaPID / peptide cyclization / OPA / mRNA display
Outline of Research at the Start

We aim to develop OPA-based cyclic peptide libraries using the FIT system. These libraries will selectively release the free reactive moiety after the translation step for peptide cyclization or PTMs, which will be further applied in the RaPID system to identify potential drug molecules. Additionally, we plan to explore a chemoselective peptide cyclization method for post-translational modifications. Through this, we aim to contribute to the development of chemical biology studies and drug discovery efforts, aimed at identifying peptide candidates against various disease-related proteins.

Outline of Annual Research Achievements

We successfully established an mRNA display-based in vitro bicyclic peptide construction platform using a flexible in vitro translation (FIT) system with novel o-phthalaldehyde amino acids that can toggle reactivity on and off during the translation process. This strategy has been demonstrated on the construction of over 20 different nonstandard peptides with various lengths and sequences in vitro, facilitating the rapid assembly of a bicyclic nonstandard peptide library with up to 10^12 unique peptide sequences.
Additionally, the applicant developed an optimized thiopeptide drug discovery platform that predominantly incorporates non-proteinogenic structural elements. This platform successfully produced natural product-like drug candidates that target the Traf2- and NCK-interacting kinase (TNIK); a protein implicated in several forms of cancer. These candidates not only demonstrate high affinity and inhibitory activity (best KD = 2.1 nM, best IC50 = 0.15 μM) but also significant metabolic stability human serum (half-life of up to 99 hours).

Current Status of Research Progress
Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

We are currently evaluating the cyclization limits of our strategy by analyzing various model peptide RNA sequences to determine the optimal cyclization sites and nearby amino acid combinations. Subsequently, we are applying this novel strategy to construct nonstandard peptide libraries, characterized by densely functionalized structures reminiscent of natural products. We will assemble and screen a large combinatorial library of bicyclic peptides against TNIK protein, and thymic stromal lymphopoietin (TSLP), which plays a crucial role in the pathogenesis of immediate-type allergy. Our goal is to identify a series of compounds that act as potent and selective inhibitors. Currently, we are focused on the novel library design and are nearing completion of the library assembly. We will commence the new phase of bicyclic nonstandard peptide drug discovery targeting these two proteins within few months.

Strategy for Future Research Activity

1.Evaluation of Cyclization Limits: We will assess the cyclization efficiency of our established OPA-based in vitro bicyclic peptide construction strategy, which utilizes the flexible in vitro translation (FIT) system to synthesize OPA-based novel non-proteinogenic amino acid-containing peptides. These peptides spontaneously cyclize with internal cysteine and lysine residues to form stable bicyclic structures. Our goal is to determine the optimal cyclization sites for both cysteine and lysine residues across different peptide sequences and structures.
2.Construction of a Bicyclic Nonstandard Peptide Library: Utilizing the optimized OPA-based in vitro method, we aim to construct various libraries that feature complex, densely functionalized structures reminiscent of natural products. This approach enables the establishment of large numbers of nonstandard peptides (>10^12 unique compounds) for early-stage peptide drug discovery.
3.Affinity Selection Against Disease-Related Protein Targets: Leveraging the established OPA-based bicyclic peptide library in combination with the random nonstandard peptide integrated discovery (RaPID) system, our focus is on rapid early-stage drug discovery targeting both cancer and allergy-related proteins, specifically TNIK and TSLP proteins. These targets are crucial in the pathogenesis of various cancers and immediate-type allergies, respectively.

Report

(2 results)
  • 2023 Research-status Report
  • 2022 Annual Research Report
  • Research Products

    (3 results)

All 2024 2022

All Journal Article (3 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 3 results,  Open Access: 1 results)

  • [Journal Article] A Compact Reprogrammed Genetic Code for De Novo Discovery of Proteolytically Stable Thiopeptides2024

    • Author(s)
      Vinogradov Alexander A.、Zhang Yue、Hamada Keisuke、Kobayashi Shunsuke、Ogata Kazuhiro、Sengoku Toru、Goto Yuki、Suga Hiroaki
    • Journal Title

      Journal of the American Chemical Society

      Volume: 146 Issue: 12 Pages: 8058-8070

    • DOI

      10.1021/jacs.3c12037

    • Related Report
      2023 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Solid-Phase-Based Synthesis of Lactazole-Like Thiopeptides2022

    • Author(s)
      Zhang Yue、Vinogradov Alexander A.、Chang Jun Shi、Goto Yuki、Suga Hiroaki
    • Journal Title

      Organic Letters

      Volume: 24 Issue: 43 Pages: 7894-7899

    • DOI

      10.1021/acs.orglett.2c02870

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors2022

    • Author(s)
      Vinogradov Alexander A.、Zhang Yue、Hamada Keisuke、Chang Jun Shi、Okada Chikako、Nishimura Hirotaka、Terasaka Naohiro、Goto Yuki、Ogata Kazuhiro、Sengoku Toru、Onaka Hiroyasu、Suga Hiroaki
    • Journal Title

      Journal of the American Chemical Society

      Volume: 144 Issue: 44 Pages: 20332-20341

    • DOI

      10.1021/jacs.2c07937

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research

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Published: 2022-11-17   Modified: 2024-12-25  

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