研究概要

タンパク質ユビキチン化は、プロテアソームによるタンパク質分解のみならず、当初の想定を大きく超える多様なタンパク質機能制御機構であることがわかってきました。この多様な機能を生み出す基盤は、ユビキチン修飾の構造多様性と相互作用する分子（デコーダー）の多様性にあります。私たちは、ユビキチン修飾系を理解し、操作する新たな方法論を開拓することを目的として、UbTACs（ubiquitin-targeting chimeras）と名付けた新たなユビキチン化誘導キメラ分子の創製に挑戦します。具体的には、化合物アレイを用いて新規ユビキチンリガーゼ結合分子（E3リガンド）および標的ネオ基質に結合するリガンド化合物（分子弾頭）の探索・同定を行います。次いで、見出した各化合物にアジドおよびアルキン官能基を位置選択的に導入し、E3リガンドと分子弾頭の間のリンカー距離や分子配置を考慮しながらクリック反応によって両者を複合化してキメラ化合物UbTACsを開発します（図１）。得られた化合物の有効性は、領域内の他の班員と協力して解析し、より優れたものにするための化学構造の改良も計画しています。
また、ユビキチンデコーダーの機能解析のための化学的ツールを開発するため、さまざまなユビキチン修飾とその相互作用分子の間の結合を阻害する小分子の開発に挑戦します。そのためにまず、ユビキチンに特異的に結合するデコーダー分子のユビキチン結合ドメインを標的とし、ユビキチンとの相互作用を阻害する化合物の探索系を構築します。具体的には、私たち独自に最適化した二分子発光補完法（スプリットルシフェラーゼ）やTR-FRET等を用いたハイスループットスクリーニング系を開発します。次に理研天然化合物バンク（NPDepo）が保有する化合物ライブラリーを用いてユビキチンデコーダーの相互作用を阻害する化合物を探索します。得られた化合物が実際に細胞内で作用するかどうかを検証し、ケモユビキチン研究に資する優れた化合物を選択していきます。
さらに研究代表者の有するハイスループットスクリーニングシステムの利点を生かし、領域内の研究者と連携して新しいユビキチンリガーゼ阻害剤の探索にも取り組む予定です。

研究概要を示す模式図

図１．化合物アレイによるリガンド探索とキメラ化合物合成

本領域での研究成果

1. Sohtome Y, Shimazu T, Barjau J, Fujishiro S, Akakabe M, Terayama N, Dodo K, Ito A, Yoshida M, Shinkai Y, Sodeoka M.
   Unveiling epidithiodiketopiperazine as a non-histone arginine methyltransferase inhibitor by chemical protein methylome analyses.
   Chem. Commun. 54, 9202-9205 (2018)
   PMID: 30063235
2. Hiranaka S, Tega Y, Higuchi K, Kurosawa T, Deguchi Y, Arata M, Ito A, Yoshida M, Nagaoka Y, Sumiyoshi T.
   Design, Synthesis, and Blood-Brain Barrier Transport Study of Pyrilamine Derivatives as Histone Deacetylase Inhibitors.
   ACS Med. Chem. Lett. 9, 884-888 (2018)
   PMID: 30258535
3. Furuta H, Yoshihara H, Fukushima T, Yoneyama Y, Ito A, Worrall C, Girnita A, Girnita L, Yoshida M, Asano T, Komada M, Kataoka N, Chida K, Hakuno F, Takahashi SI.
   IRS-2 deubiquitination by USP9X maintains anchorage-independent cell growth via Erk1/2 activation in prostate carcinoma cell line.
   Oncotarget 9, 33871-33883 (2018)
   PMID: 30338032
4. Simpkins SW, Nelson J, Deshpande R, Li SC, Piotrowski JS, Wilson EH, Gebre AA, Safizadeh H, Okamoto R, Yoshimura M, Costanzo M, Yashiroda Y, Ohya Y, Osada H, Yoshida M, Boone C, Myers CL.
   Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions.
   PLoS Comput. Biol. 14, e1006532 (2018)
   PMID: 30376562
5. Tanei T, Pradipta AR, Morimoto K, Fujii M, Arata M, Ito A, Yoshida M, Saigitbatalova E, Kurbangalieva A, Ikeda JI, Morii E, Noguchi S, Tanaka K.
   Cascade reaction in human live tissue allows clinically applicable diagnosis of breast cancer morphology.
   Adv. Sci. 6, 1801479 (2018)
   PMID: 30693189
   プレスリリース
6. Mizutani A, Yashiroda Y, Muramatsu Y, Yoshida H, Chikada T, Tsumura T, Okue M, Shirai F, Fukami T, Yoshida M, Seimiya H.
   RK-287107, a potent and specific tankyrase inhibitor, blocks colorectal cancer cell growth in a preclinical model.
   Cancer Sci. 109, 4003-4014 (2018)
   PMID: 30238564
7. Simpkins SW, Deshpande R, Nelson J, Li SC, Piotrowski JS, Ward HN, Yashiroda Y, Osada H, Yoshida M, Boone C, Myers CL.
   Using BEAN-counter to quantify genetic interactions from multiplexed barcode sequencing experiments.
   Nat. Protoc. 14, 415-440 (2019)
   PMID: 30635653
8. Ling F, Bradshaw E, Yoshida M.
   Prevention of mitochondrial genomic instability in yeast by the mitochondrial recombinase Mhr1.
   Sci. Rep. 9, 5433 (2019)
   PMID: 30931958
9. Shirai F, Tsumura T, Yashiroda Y, Yuki H, Niwa H, Sato S, Chikada T, Koda Y, Washizuka K, Yoshimoto N, Abe M, Onuki T, Mazaki Y, Hirama C, Fukami T, Watanabe H, Honma T, Umehara T, Shirouzu M, Okue M, Kano Y, Watanabe T, Kitamura K, Shitara E, Muramatsu Y, Yoshida H, Mizutani A, Seimiya H, Yoshida M, Koyama H.
   Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors.
   J. Med. Chem. 62, 3407-3427 (2019)
   PMID: 30883102
10. Murashima A, Shinjo K, Katsushima K, Onuki T, Kondoh Y, Osada H, Kagaya N, Shin-Ya K, Kimura H, Yoshida M, Murakami S, Kondo Y.
    Identification of a chemical modulator of EZH2-mediated silencing by cell-based high-throughput screening assay.
    J. Biochem. 166, 41-50 (2019)
    PMID: 30690451
11. Mitsui E, Yoshida S, Shinoda Y, Matsumori Y, Tsujii H, Tsuchida M, Wada S, Hasegawa M, Ito A, Mino K, Onuki T, Yoshida M, Sasaki R, Mizukami T.
    Identification of ryuvidine as a KDM5A inhibitor.
    Sci. Rep. 9, 9952 (2019)
    PMID: 31289306
12. Takase S, Kurokawa R, Kondoh Y, Honda K, Suzuki T, Kawahara T, Ikeda H, Dohmae N, Osada H, Shin-Ya K, Kushiro T, Yoshida M, Matsumoto K.
    Mechanism of action of prethioviridamide, an anticancer ribosomally synthesized and post-translationally modified peptide with a polythioamide structure.
    ACS Chem. Biol. 14, 1819-1828 (2019)
    PMID: 31365229
13. Han P, Shichino Y, Schneider-Poetsch T, Mito M, Hashimoto S, Udagawa T, Kohno K, Yoshida M, Mishima Y, Inada T, *Iwasaki S.
    Genome-wide survey of ribosome collision.
    Cell Rep. 31, 107610 (2020)
    PMID: 32375038
14. Jo T, *Nishikori M, Kogure Y, Arima H, Sasaki K, Sasaki Y, Nakagawa T, Iwai F, Momose S, Shiraishi A, Kiyonari H, Kagaya N, Onuki T, Shin-Ya K, Yoshida M, Kataoka K, Ogawa S, *Iwai K, Takaori-Kondo A.
    LUBAC accelerates B-cell lymphomagenesis by conferring resistance to genotoxic stress on B cells.
    Blood 136, 684-697 (2020)
    PMID: 32325488
15. Radwan MO, Ciftci HI, Ali TFS, Koga R, Tateishi H, Nakata A, Ito A, Yoshida M, Fujita M, *Otsuka M.
    Structure activity study of S-trityl-cysteamine dimethylaminopyridine derivatives as SIRT2 inhibitors: Improvement of SIRT2 binding and inhibition.
    Bioorg. Med. Chem. Lett. 30,127458 (2020)
    PMID: 32755678
16. Kobayashi H, Nishimura H, Kudo N, Osada H, *Yoshida M.
    A novel GSK3 inhibitor that promotes self-renewal in mouse embryonic stem cells.
    Biosci. Biotechnol. Biochem. 84, 2113-2120 (2020)
    PMID: 32640867
17. Kobayashi H, Hatakeyama H, Nishimura H, Yokota M, Suzuki S, Tomabechi Y, Shirouzu M, Osada H, Mimaki M, *Goto Y, *Yoshida M.
    Chemical reversal of abnormalities in cells carrying mitochondrial DNA mutations.
    Nat. Chem. Biol. 171,335-343 (2021)
    PMID: 33168978
    プレスリリース
18. Yoshimoto R, Chhipi-Shrestha JK, Schneider-Poetsch T, Furuno M, Maxwell Burroughs A, Noma S, Suzuki H, Hayashizaki Y, Mayeda A, Nakagawa S, Kaida D, Iwasaki S, *Yoshida M.
    Spliceostatin A interaction with SF3B1 limits U1 snRNP availability and causes premature cleavage and polyadenylation.
    Cell Chem. Biol. 28, 1356-1365 (2021)
    PMID: 33784500
    プレスリリース
19. Takayama KI, Honma T, Suzuki T, Kondoh Y, Osada H, Suzuki Y, Yoshida M, Inoue S.
    Targeting Epigenetic and Posttranscriptional Gene Regulation by PSF Impairs Hormone Therapy-Refractory Cancer Growth.
    Cancer Res. 81, 3495-3508 (2021)
    PMID: 33975881
20. Nakatani K, Maehama T, Nishio M, Otani J, Yamaguchi K, Fukumoto M, Hikasa H, Hagiwara S, Nishina H, Mak TW, Honma T, Kondoh Y, Osada H, Yoshida M, Suzuki A.
    Alantolactone is a natural product that potently inhibits YAP1/TAZ through promotion of reactive oxygen species accumulation.
    Cancer Sci. 112, 4303-4316 (2021)
    PMID: 34289205
21. Chhipi-Shrestha JK, Schneider-Poetsch T, Suzuki T, Mito M, Khan K, Dohmae N, *Iwasaki S, *Yoshida M.
    Splicing modulators elicit global translational repression by condensate-prone proteins translated from introns.
    Cell Chem. Biol. 29, 259-275 (2022)
    PMID: 34520743
    プレスリリース
22. Sasaki K, Suzuki M, Sonoda T, Schneider-Poetsch T, Ito A, Takagi M, Fujishiro S, Sohtome Y, Dodo K, Umehara T, Aburatani H, Shin-ya K, Nakao Y, Sodeoka M, *Yoshida M.
    Visualization of the dynamic interaction between nucleosomal histone H3K9 tri-methylation and HP1α chromodomain in living cells.
    Cell Chem. Biol. 29, 1153-1161 (2022)
    PMID: 35728598
    プレスリリース
23. Kato H, Nemoto K, Shimizu M, Abe A, Asai S, Ishihama N, Matsuoka S, Daimon T, Ojika M, Kawakita K, Onai K, Shirasu K, Yoshida M, Ishiura M, Takemoto D, Takano Y, Terauchi R.
    Recognition of pathogen-derived sphingolipids in Arabidopsis.
    Science. 376, 857-860 (2022)
    PMID: 35587979
    プレスリリース
24. Chhipi-Shrestha JK, Yoshida M, Iwasaki S.
    Filter trapping protocol to detect aggregated proteins in human cell lines.
    STAR Protoc. 3, 101571 (2022)
    PMID: 35880124
25. Manzoor M, Muroi M, Ogawa N, Kobayashi H, Nishimura H, Chen D, Fasina OB, Wang J, Osada H, Yoshida M, Xiang L, Qi J.
    Isoquercitrin from Apocynum venetum L. produces an anti-obesity effect on obese mice by targeting C-1-tetrahydrofolate synthase, carbonyl reductase, and glutathione S-transferase P and modification of the AMPK/SREBP-1c/FAS/CD36 signaling pathway in mice in vivo.
    Food Funct. 13, 10923-10936 (2022)
    PMID: 36205648

代表的な論文

1. Nishimura S, Arita Y, Honda M, Iwamoto K, Matsuyama A, Shirai A, Kawasaki H, Kakeya H, Kobayashi T, Matsunaga S, *Yoshida M.
   Marine antifungal theonellamides target 3ß-hydroxysterol to activate Rho1 signaling.
   Nat. Chem. Biol. 6, 519-526 (2010)
   PMID: 20543850
2. Ito A, Shimazu T, Maeda S, Shah AA, Tsunoda T, Iemura S-I, Natsume T, Suzuki T, Motohashi H, Yamamoto M, *Yoshida M.
   The subcellular localization and activity of cortactin is regulated by acetylation and interaction with Keap1.
   Sci. Signal. 8, ra120(2015)
   PMID: 26602019
3. Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H, Gebre AA, Kubo K, Torres N, Leblanc MB, Andrusiak K, Okamoto R, Yoshimura M, van Leeuwen J, Shirahige K, Baryshnikova A, Brown G, Saito T, Costanzo M, Andrews B, Ohya Y, *Osada H, *Yoshida M, *Myers CL, *Boone C.
   Functional annotation of chemical libraries across diverse biological processes.
   Nat. Chem. Biol. 13, 982-993 (2017)
   PMID: 28759014
4. Tanei T, Pradipta AR, Morimoto K, Fujii M, Arata M, Ito A, Yoshida M, Saigitbatalova E, Kurbangalieva A, Ikeda JI, Morii E, Noguchi S, *Tanaka K.
   Cascade reaction in human live tissue allows clinically applicable diagnosis of breast cancer morphology.
   Adv. Sci. 6, 1801479 (2018)
   PMID: 30693189
5. Schneider-Poetsch T, Usui T, Kaida D, *Yoshida M.
   Garbled messages and corrupted translations.
   Nat. Chem. Biol. 6, 189-198 (2010)
   PMID: 20154667