• 文部科学省
  • JSPS
  • 科研費
  • ユビキチンネオバイオロジー
  • ユビキチンネオバイオロジー
Research Group

Research Group

Team

Research Group

Research group A02: Development of ubiquitin chemo-technologies

Development of chemical protein knockdown technologies and their application to manipulate cellular functions

Mikihiko Naito

Mikihiko Naito, PhD

Graduate School of Pharmaceutical Sciences, The University of Tokyo
Project Professor
https://tpd.f.u-tokyo.ac.jp

Yosuke Demizu

Yosuke Demizu, PhD

Division of Organic Chemistry, National Institute of Health Sciences
Chief
http://www.nihs.go.jp/doc/index.html

Minoru Ishikawa

Minoru Ishikawa, PhD

Graduate School of Life Sciences, Tohoku University
Professor
https://www.agri.tohoku.ac.jp/ishikawa-lab/index.html

Takumi Ito

Takumi Ito, PhD

Department of Chemical Biology, Tokyo Medical University
Associate Professor
http://www.tokyo-med.ac.jp/nanoparticle/engindex.html

We have established chemical protein knockdown technologies that utilize compounds such as SNIPERs (Specific and Nongenetic IAP-dependent Protein Erasers) and cereblon (CRBN) modulators
(also known as IMiDs immunomodulators) to induce ubiquitylation and proteasomal degradation of target proteins in cells. SNIPER is a chimeric compound consisting of a ligand (IAP antagonist) that binds to an IAP and a ligand (molecular warhead) that binds to a target protein, which induces ubiquitylation by recruiting an IAP ubiquitin ligase to the target protein. It is a highly versatile technology that can target and degrade various target proteins by replacing molecular warheads. The CRBN modulator, on the other hand, is a compound that binds to CRBN, the substrate recognition molecule of CRL4CRBN ubiquitin ligase, and modulates its substrate specificity. These compounds have recently been shown to be able to induce various cellular responses involving ubiquitin, including not only degradation but also internalization of receptors on cell surface.
In this study, we are challenging to elucidate the principle of the ubiquitin code by using chemical protein knockdown technologies to ubiquitylate various target proteins and analyze the cellular responses, which includes the following subjects.

1. Development and expansion of SNIPER technology

2. Analysis of ubiquitin coding mechanism using SNIPER and other compounds

3. Development of the CRBN modulators and the mechanism of teratogenicity and therapeutic effect

4.Structural analysis of E3 ligase and neo-substrate complexes formed by SNIPER

5. Development of mitophagy induction technology

研究概要を示す模式図

Publications

  1. Nishiyama Y, Fujii S, Makishima M, Hashimoto Y, Ishikawa M.
    Efficient lead finding, activity enhancement and preliminary selectivity control of nuclear receptor ligands bearing a phenanthridinone skeleton.
    Int. J. Mol. Sci. 19, 2090 (2018)
    PMID: 30021999
  2. Shibata N, Shimokawa K, Nagai K, Ohoka N, Hattori T, Miyamoto N, Ujikawa O, Sameshima T, Nara H, Cho N, Naito M.
    Pharmacological difference between degrader and inhibitor against oncogenic BCR-ABL kinase.
    Sci. Rep. 8, 13549 (2018)
    PMID: 30202081
  3. Shioi R, Toyota Y, Noguchi-Yachide T, Ishikawa M,Yamaguchi T, Makishima M, Hashimoto Y, Ohgane K.
    Unexpected emergence of luciferase-inhibitory activity during structural development study of phenyloxadiazole-based PPAR ligands.
    Heterocycles 97, 854-864 (2018)
  4. Misawa T, Goto C, Shibata N, Hirano M, Kikuchi Y, Naito M, Demizu Y.
    Rational design of novel amphipathic antimicrobial peptides focused on distribution of cationic amino acid residues.
    MedChemComm 10, 896-900 (2019)
    PMID: 31303986
  5. Ohoka N, Ujikawa O, Shimokawa K, Sameshima T, Shibata N, Hattori T, Nara H, Cho N, Naito M.
    Different Degradation Mechanisms of Inhibitor of Apoptosis Proteins (IAPs) by the Specific and Nongenetic IAP-Dependent Protein Eraser (SNIPER).
    Chem. Pharm. Bull. 67, 203-209 (2019)
    PMID: 30369550
  6. Ando H, Sato T, Ito T, Yamamoto J, Sakamoto S, Nitta N, Asatsuma-Okumura T, Shimizu N, Mizushima R, Aoki I, Imai T, Yamaguchi Y, Berk AJ, Handa H.
    Cereblon Control of Zebrafish Brain Size by Regulation of Neural Stem Cell Proliferation.
    iScience 15, 95-108 (2019)
    PMID: 31055217
  7. Misawa T, Ohoka N, Oba M, Yamashita H, Tanaka M, Naito M, Demizu Y.
    Development of 2-aminoisobutyric acid (Aib)-rich cell-penetrating foldamers for efficient siRNA delivery.
    Chem. Commun. 55, 7792-7795 (2019)
    PMID: 31210205
  8. Asatsuma-Okumura T, Ando H, De Simone M, Yamamoto J, Sato T, Shimizu N, Asakawa K, Yamaguchi Y, Ito T, Guerrini L, Handa H.
    p63 is a cereblon substrate involved in thalidomide teratogenicity.
    Nat. Chem. Biol. 15, 1077-1084 (2019)
    PMID: 31591562
  9. Ohoka N, Tsuji G, Shoda T, Fujisato T, Kurihara M, Demizu Y, Naito M.
    Development of Small Molecule Chimeras That Recruit AhR E3 Ligase to Target Proteins.
    ACS Chem. Biol. 14, 2822-2832 (2019)
    PMID: 31580635
  10. Goto C, Hirano M, Hayashi K, Kikuchi Y, Hara-Kudo Y, Misawa T, Demizu Y.
    Development of amphipathic antimicrobial peptide foldamers based on Magainin 2 sequence.
    ChemMedChem 14, 1911-1916 (2019)
    PMID: 31667994
  11. Yamashita H, Tomoshige S, Nomura S, Ohgane K, Hashimoto Y, Ishikawa M.
    Application of Protein Knockdown Strategy Targeting β-Sheet Structure to Multiple Disease-associated Polyglutamine Proteins.
    Bioorg. Med. Chem. 28, 115175 (2020)
    PMID: 31767406
  12. Tateno S, Iida M, Fujii S, Suwa T, Katayama M, Tokuyama H, Yamamoto J, Ito T, Sakamoto S, Handa H, Yamaguchi Y.
    Genome-wide screening reveals a role for subcellular localization of CRBN in the anti-myeloma activity of pomalidomide.
    Sci. Rep. 10, 4012 (2020)
    PMID: 32132601
  13. *Shoda T, Ohoka N, Tsuji G, Fujisato T, Inoue H, Demizu Y, Naito M, Kurihara M.
    Targeted protein degradation by chimeric compounds using hydrophobic E3 ligands and adamantane moiety.
    Pharmaceuticals 13, 34 (2020)
    PMID: 32106507
  14. Shibata N, Ohoka N, Tsuji G, Demizu Y, Akiyama T, *Naito M.
    Deubiquitylase USP25 prevents degradation of BCR-ABL protein and ensures proliferation of Ph-positive leukemia cells.
    Oncogene 39, 3867-3878 (2020)
    PMID: 32203161
  15. Yokoo H, Ohoka N, Naito M, *Demizu Y.
    Design and synthesis of peptide-based chimeric molecules to induce degradation of the estrogen and androgen receptors.
    Bioorg. Med. Chem. 28, 115595 (2020)
    PMID: 32631565
  16. Yamamoto J, Suwa T, Murase Y, Tateno S, Mizutome H, Asatsuma-Okumura T, Shimizu N, Kishi T, Momose S, Kizaki M, Ito T, *Yamaguchi Y, *Handa H.
    ARID2 is a pomalidomide-dependent CRL4CRBN substrate in multiple myeloma cells.
    Nat. Chem. Biol. 16, 1208-1217 (2020)
    PMID: 32958952
  17. *Yamano K, Kikuchi R, Kojima W, Hayashida R, Koyano F, Kawakami J, Shoda T, Demizu Y, Naito M, Tanaka K, Matsuda N.
    Critical role of mitochondrial ubiquitination and the OPTN-ATG9A axis in mitophagy.
    J. Cell Biol. 219, e201912144 (2020)
    PMID: 32556086
  18. Hirano M, Saito C, Goto C, Yokoo H, Kawano R, *Misawa T, *Demizu Y.
    Rational design of helix-stabilized antimicrobial peptide foldamers containing a,a-disubstituted amino acids or side-chain stapling.
    ChemPlusChem 85,2731-2736 (2020)
    PMID: 33369262
  19. Yokoo H,# Shibata N,# Naganuma M, Murakami Y, Ito T, *Aritake K, *Naito M, *Demizu Y.
    Development of hematopoietic prostaglandin D synthase-degradation inducer.
    ACS Med. Chem. Lett. 12,236-241 (2021)
    PMID: 33603969
    # These authors equally contributed to this work.
    <Selected as Supplementary Cover>
  20. Hirano M, Saito C, Yokoo H, Goto C, Kawano R, *Misawa T, *Demizu Y.
    Structure-activity relationship analysis of Mag2-based peptide foldamers.
    Molecules 26,444 (2021)
    PMID: 33466998
  21. Soma-Kaiho A, Akizuki Y, Igarashi K, Endo A, Kawase Y, Shoda T, Demizu Y, Naito M, Saeki Y, Tanaka K, *Ohtake F.
    TRIP12 enhances small molecule-induced degradation of BRD4 through K29/K48 branched ubiquitin chains.
    Mol. Cell, 81, 1411-1424.e7 (2021)
    PMID: 33567268
  22. Ichikawa Y, Hiramatsu M, Mita Y, Makishima M, Matsumoto Y, Masumoto Y, Muranaka A, Uchiyama M, Hashimoto Y, *Ishikawa M.
    meta-Non-flat substituents: a novel molecular design to improve aqueous solubility in small molecule drug discovery.
    Org. Biomol. Chem. 19, 446-456 (2021)
    PMID: 33331380
  23. Tsukumo Y,#Tsuji G,#Yokoo H, Shibata N, Ohoka N, Demizu Y, *Naito M.
    Protocols for synthesis of SNIPERs and the methods to evaluate the anticancer effects.
    Methods Mol. Biol. 2365, 331-347 (2021)
    PMID: 34432253
    #These authors equally contributed to this work.
  24. Xu H,#Ohoka N,#Yokoo H, Nemoto K, Ohtsuki T, Matsufuji H, Naito M, Inoue T, *Tsuji G, *Demizu Y.
    Development of agonist-based PROTACs targeting liver X receptor.
    Front. Chem. 9, 674967 (2021)
    PMID: 34124002
    #These authors equally contributed to this work.
  25. Nakane K, *Sato S, Niwa T, Tsushima M, Tomoshige S, Taguchi H, Ishikawa M, Nakamura H.
    Proximity Histidine Labeling by Umpolung Strategy Using Singlet Oxygen.
    J. Am. Chem. Soc. 143, 7726-7731 (2021)
    PMID: 33904715
  26. Morimoto J, Miyamoto K, Ichikawa Y, Uchiyama M, Makishima M, Hashimoto Y, *Ishikawa M.
    Improvement in aqueous solubility of achiral symmetric cyclofenil by modification to a chiral asymmetric analog.
    Sci. Rep. 11, 12697 (2021)
    PMID: 34135380
  27. *Yokoo H, Hirano M, Ohoka N, Misawa T, *Demizu Y.
    Structure-activity relationship study of amphipathic antimicrobial peptides using helix-destabilizing sarcosine.
    J. Pept. Sci. e3360, 1-6 (2021)
    PMID: 34164880
  28. Obara S, Nakane K, Fujimura C, Tomoshige S, Ishikawa M, *Sato S.
    Functionalization of Human Serum Albumin by Tyrosine Click.
    Int. J. Mol. Sci. 22, 8676-8676 (2021)
    PMID: 34445381
  29. Yokoo H,#Ohoka N,#Takyo M, Ito T, Tsuchiya K, Kurohara T, Fukuhara K, Inoue T, Naito M, *Demizu Y.
    Peptide stapling improves the sustainability of a peptide-based chimeric molecule that induces targeted protein degradation.
    Int. J. Mol. Sci. 22, 8772 (2021)
    PMID: 34445478
    #These authors equally contributed to this work.
  30. Yokoo H, *Shibata N, Endo A, Ito T, Yanase Y, Murakami Y, Fujii K, Hamamura K, Saeki Y, *Naito M, *Aritake K, *Demizu Y.
    Discovery of a highly potent and selective PROTAC targeting hematopoietic prostaglandin D synthase via in silico design.
    J. Med. Chem. 64, 15868-15882 (2021)
    <Selected as Supplementary Cover>
  31. Shimizu N, Asatuma-Okumura T, Yamamoto J, Yamaguchi Y, *Handa H,*Ito T.
    PLZF and its fusion proteins are pomalidomide-dependent CRBN neosubstrates.
    Commun Biol. 4, 1277 (2021)
    PMID: 34764413
  32. Naganuma M, *Ohoka N, Tsuji G, Tsujimura H, Matsuno K, Inoue T, Naito M,  *Demizu Y.
    Development of chimeric molecules that degrade the estrogen receptor using decoy oligonucleotide ligands.
    ACS Med. Chem. Lett. 13, 134-139 (2022)
    PMID: 35059133
    <Selected as Supplementary Cover>
  33. #Ohoka N, #Yokoo H,  Okuhira K, Demizu Y, *Naito M.
    Molecular design, synthesis and evaluation of SNIPER(ER) that induces targeted protein degradation of ER α.
    Methods Mol. Biol. 2418, 363-382 (2022)
    PMID: 35119675
    #These authors equally contributed to this work.
  34. Hirai K, Yamashita H, *Tomoshige S, Mishima Y, Niwa T, Ohgane K, Ishii M, Kanamitsu K, Ikemi Y, Nakagawa S, Taguchi H, Sato S, Hashimoto Y, *Ishikawa M.
    Conversion of a PROTAC mutant huntingtin degrader into small-molecule hydrophobic tags focusing on drug-like properties.
    ACS Med. Chem. Lett. 13, 396-402 (2022)
    PMID: 35300080
  35. Shibata N, Cho N, Koyama H, Naito M.
    Development of a degrader against oncogenic fusion protein FGFR3-TACC3.
    Bioorg Med Chem Lett 60, 128584 (2022)
    PMID: 35085722

    Former Publications

    1. Ito T, Ando H, Suzuki T, Ogura T, Hotta K, Imamura Y, Yamaguchi Y, *Handa H.
      Identification of a primary target of thalidomide teratogenicity.
      Science 327, 1345-1350 (2010)
      PMID: 20223979
    2. Itoh Y, Ishikawa M, Naito M, *Hashimoto Y.
      Protein knockdown using methyl bestatin-ligand hybrid molecules: design and synthesis of inducers of ubiquitination-mediated degradation of cellular retinoic acid-binding proteins.
      J. Am. Chem. Soc. 132, 5820-5826 (2010)
      PMID: 20369832
    3. Matyskiela ME, *Lu G, Ito T (co-1st author), Pagarigan B, Lu C-C, Miller K, Fang W, Wang NY, Nguyen D, Houston J, Carmel G, Tran T, Riley M, Nosaka L, Lander GC, Gaidarova S, Xu S, Ruchelman AL, Handa H, Carmichael J, Daniel TO, Cathers BE, Lopez-Girona A, *Chamberlain PP.
      A novel cereblon modulator recruits GSPT1 to the CRL4CRBN ubiquitin ligase.
      Nature 535, 252-257 (2016)
      PMID: 27338790
    4. Yamashita H, Kato T, Oba M, Misawa T, Hattori T, Ohoka N, Tanaka M, Naito M, *Kurihara M, *Demizu Y.
      Development of a cell-penetrating peptide that exhibits responsive changes in its secondary structure in the cellular environment.
      Sci. Rep. 6, 33003 (2016)
      PMID: 27609319
    5. Tomoshige S, Nomura S, Ohgane K, Hashimoto Y, *Ishikawa M.
      Discovery of small molecules that induce the degradation of huntingtin.
      Angew. Chem. Int. Ed. 56, 11530-11533 (2017)
      PMID: 28703441
    6. Okuhira K, Shoda T, Omura R, Ohoka N, Hattori T, Shibata N, Demizu Y, Sugihara R, Ichino A, Kawahara H, Itoh Y, Ishikawa M, Hashimoto Y, Kurihara M, Itoh S, Saito H, *Naito M.
      Targeted degradation of proteins localized in subcellular compartments by hybrid small molecules.
      Mol. Pharmacol. 91, 159-166 (2017)
      PMID: 27965304
    7. Ohoka N, Okuhira K, Ito M, Nagai K, Shibata N, Hattori T, Ujikawa O, Shimokawa K, Sano O, Koyama R, Fujita H, Teratani M, Matsumoto H, Imaeda Y, Nara H, Cho N, *Naito M.
      In vivo knockdown of pathogenic proteins via specific and nongenetic inhibitor of apoptosis protein (IAP)-dependent protein erasers (SNIPERs).
      J. Biol. Chem. 292, 4556-4570 (2017)
      PMID: 28154167
    8. Mori T, Ito T (co-1st author), Liu S, Ando H, Sakamoto S, Yamaguchi Y, Tokunaga E, Shibata N, *Handa H, *Hakoshima T.
      Structural basis of thalidomide enantiomer binding to cereblon.
      Sci. Rep. 8, 1294 (2018)
      PMID: 29358579
    9. Okitsu K, Hattori T, Misawa T, Shoda T, Kurihara M, *Naito M, *Demizu Y.
      Development of a small hybrid molecule that mediates degradation of His-tag fused proteins.
      J. Med. Chem. 61, 576-582 (2018)
      PMID: 28460164
    10. Shibata N, Nagai K, Morita Y, Ujikawa O, Ohoka N, Hattori T, Koyama R, Sano O, Imaeda Y, Nara H, Cho N, *Naito M.
      Development of protein degradation inducers of androgen receptor by conjugation of androgen receptor ligands and inhibitor of apoptosis protein ligands.
      J. Med. Chem. 61, 543-575 (2018)
      PMID: 28594553
    11. Nishiyama Y, Mori S, Makishima M, Fujii S, Kagechika H, Hashimoto Y, *Ishikawa M.
      Novel nonsteroidal progesterone receptor (PR) antagonists with a phenanthridinone skeleton.
      ACS Med. Chem. Lett. 9, 641-645 (2018)
      PMID: 30034593