Yuki Goto, Ph.D.

Associate Professor



B.Sc., Faculty of Engineering, Kyoto University
Thesis advisor: Prof. Isao Saito
M.Sc., Graduate School of Engineering, Kyoto University
Thesis advisor: Prof. Kazuhiko Nakatani
Ph.D., Graduate School of Engineering, The University of Tokyo
Thesis advisor: Prof. Hiroaki Suga

Professional career

Research Fellow of the Japan Society for the Promotion of Science
Postdoctoral research associate, University of Illinois at Urbana-Champaign (JSPS Postdoctoral Fellow for Research Abroad)
Advisor: Prof. Wilfred A. van der Donk
Assistant professor, Research Center for Advanced Science and Technology, The University of Tokyo
Assistant professor, Graduate School of Science, The University of Tokyo
Investigator, PRESTO (Design and Control of Cellular Functions), Japan Science and Technology Agency

Contact Info

  • Room #2208, West wing, Chemistry Bildg.
    Department of Chemistry, Graduate School of Science, The University of Tokyo
  • E-mail… y-goto"at"chem.s.u-tokyo.ac.jp (change "at" to @)
  • TEL…+81-3-5841-4338
  • FAX…+81-3-5841-8372

Publication (Journal articles)

"Highly selective inhibition of histone demethylases by de novo macrocyclic peptides."
A. Kawamura; M. Munzel; T. Kojima; C. Yapp; B. Bhushan; Y. Goto; A. Tumber; T. Katoh; O.N. King; T. Passioura; L.J. Walport; S.B. Hatch; S. Madden; S. Muller; P.E. Brennan; R. Chowdhury; R.J. Hopkinson; H. Suga; C.J. Schofield
Nature Communications, 8, 14773 (2017)
"Dissection of goadsporin biosynthesis by in vitro reconstitution leading to designer analogues expressed in vivo."
T. Ozaki; K. Yamashita; Y. Goto; M. Shimomura; S. Hayashi; S. Asamizu; Y. Sugai; H. Ikeda; H. Suga; H. Onaka
Nature Communications, 8, 14207 (2017)
"Characterization of the stereochemical configuration of lanthionines formed by the lanthipeptide synthetase GeoM."
N. Garg; Y. Goto; T. Chen; W.A. van der Donk
Biopolymers, 106, 834-842 (2016)
"Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes."
Y. Iwane; A. Hitomi; H. Murakami; T. Katoh; Y. Goto; H. Suga
Nature chemistry, 8, 317-325 (2016)
"Ribosomal synthesis of peptides with multiple beta-amino acids."
T. Fujino; Y. Goto; H. Suga; H. Murakami
J. Am. Chem. Soc., 138, 1962-1969 (2016)
"Homologous trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine/threonine misactivation."
Z. Liu; O. Vargas-Rodriguez; Y. Goto; E.M. Novoa; L. Ribas de Pouplana; H. Suga; K. Musier-Forsyth
Proceedings of the National Academy of Sciences of the United States of America, 112, 6027-6032 (2015)
"A Fluorescent Imaging Probe Based on a Macrocyclic Scaffold That Binds to Cellular EpCAM."
K. Iwasaki; Y. Goto; T. Katoh; T. Yamashita; S. Kaneko; H. Suga
Journal of molecular evolution, 81, 210-217 (2015)
"Recent developments of engineered translational machineries for the incorporation of non-canonical amino acids into polypeptides."
N. Terasaka; Y. Iwane; A.S. Geiermann; Y. Goto; H. Suga
International journal of molecular sciences, 16, 6513-6531 (2015)
"Ancestral AlaX editing enzymes for control of genetic code fidelity are not tRNA-specific."
E.M. Novoa; O. Vargas-Rodriguez; S. Lange; Y. Goto; H. Suga; K. Musier-Forsyth; L. Ribas de Pouplana
The Journal of biological chemistry, 290, 10495-10503 (2015)
"Selection-based discovery of macrocyclic peptides for the next generation therapeutics."
T. Morioka; N.D. Loik; C.J. Hipolito; Y. Goto; H. Suga
Current opinion in chemical biology, 26C, 34-41 (2015)
"Structural basis for potent inhibition of SIRT2 deacetylase by a macrocyclic peptide inducing dynamic structural change."
K. Yamagata; Y. Goto; H. Nishimasu; J. Morimoto; R. Ishitani; N. Dohmae; N. Takeda; R. Nagai; I. Komuro; H. Suga; O. Nureki
Structure, 22, 345-352 (2014)
"Selection-based discovery of druglike macrocyclic peptides."
T. Passioura; T. Katoh; Y. Goto; H. Suga
Annu. Rev. Biochem., 83, 727-752 (2014)
"One-pot synthesis of azoline-containing peptides in a cell-free translation system integrated with a posttranslational cyclodehydratase."
Y. Goto; Y. Ito; Y. Kato; S. Tsunoda; H. Suga
Chem. Biol., 21, 766-774 (2014)
"Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution."
B.J. Desai; Y. Goto; A. Cembran; A.A. Fedorov; S.C. Almo; J. Gao; H. Suga; J.A. Gerlt
Proc. Natl. Acad. Sci. USA, 111, 15066-15071 (2014)
"Distinct tRNA recognition strategies used by a homologous family of editing domains prevent mistranslation."
M. Das; O. Vargas-Rodriguez; Y. Goto; H. Suga; K. Musier-Forsyth
Nucleic Acids Res., 42, 3943-3953 (2014)
"Nonstandard peptide expression under the genetic code consisting of reprogrammed dual sense codons."
Y. Goto; M. Iseki; A. Hitomi; H. Murakami; H. Suga
ACS Chem. Biol., 8, 2630-2634 (2013)
"Reevaluation of the D-amino acid compatibility with the elongation event in translation."
T. Fujino; Y. Goto; H. Suga; H. Murakami
J. Am. Chem. Soc., 135, 1830-1837 (2013)
"Charging of tRNAs using ribozymes and selection of cyclic peptides containing thioethers."
P.C. Reid; Y. Goto; T. Katoh; H. Suga
Methods Mol. Biol., 805, 335-348 (2012)
"Selective thioether macrocyclization of peptides having the N-terminal 2-chloroacetyl group and competing two or three cysteine residues in translation."
K. Iwasaki; Y. Goto; T. Katoh; H. Suga
Org. Biomol. Chem., 10, 5783-5786 (2012)
"Flexizymes as a tRNA acylation tool facilitating genetic code reprogramming."
Y. Goto; H. Suga
Methods Mol. Biol., 848, 465-478 (2012)
"Lantibiotics from Geobacillus thermodenitrificans."
N. Garg; W. Tang; Y. Goto; S.K. Nair; W.A. van der Donk
Proc. Natl. Acad. Sci. USA, 109, 5241-5246 (2012)
"Natural product-like macrocyclic N-methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library."
Y. Yamagishi; I. Shoji; S. Miyagawa; T. Kawakami; T. Katoh; Y. Goto; H. Suga
Chem. Biol., 18, 1562-1570 (2011)
"Ribosomal synthesis of backbone-macrocyclic peptides containing gamma-amino acids."
Y. Ohshiro; E. Nakajima; Y. Goto; S. Fuse; T. Takahashi; T. Doi; H. Suga
Chembiochem, 12, 1183-1187 (2011)
"Ribosomal synthesis of backbone macrocyclic peptides."
T. Katoh; Y. Goto; M.S. Reza; H. Suga
Chem. Commun., 47, 9946-9958 (2011)
"Mechanistic studies of Ser/Thr dehydration catalyzed by a member of the LanL lanthionine synthetase family."
Y. Goto; A. Okesli; W.A. van der Donk
Biochemistry, 50, 891-898 (2011)
"Preparation of materials for flexizyme reactions and genetic code reprogramming."
Y. Goto; T. Katoh; H. Suga
Protoc. Exchange, 779-790 (2011)
"Flexizymes for genetic code reprogramming."
Y. Goto; T. Katoh; H. Suga
Nat. Protoc., 6, 779-790 (2011)
"Ribosome evolution for two artificial amino acids in E. coli."
G. Hayashi; Y. Goto; H. Suga
Chem. Biol., 17, 320-321 (2010)
"Discovery of unique lanthionine synthetases reveals new mechanistic and evolutionary insights."
Y. Goto; B. Li; J. Claesen; Y. Shi; M.J. Bibb; W.A. van der Donk
PLoS Biol., 8, e1000339 (2010)
"Ribosomal synthesis of cyclic peptides with a fluorogenic oxidative coupling reaction."
Y. Yamagishi; H. Ashigai; Y. Goto; H. Murakami; H. Suga
Chembiochem, 10, 1469-1472 (2009)
"Ribosomal synthesis of peptides with C-terminal lactams, thiolactones, and alkylamides."
E. Nakajima; Y. Goto; Y. Sako; H. Murakami; H. Suga
Chembiochem, 10, 1186-1192 (2009)
"Translation initiation with initiator tRNA charged with exotic peptides."
Y. Goto; H. Suga
J. Am. Chem. Soc., 131, 5040-5041 (2009)
"Ribosomal synthesis of dehydrobutyrine- and methyllanthionine-containing peptides."
Y. Goto; K. Iwasaki; K. Torikai; H. Murakami; H. Suga
Chem. Commun., 3419-3421 (2009)
"Ribosomal synthesis of peptidase-resistant peptides closed by a nonreducible inter-side-chain bond."
Y. Sako; Y. Goto; H. Murakami; H. Suga
ACS Chem. Biol., 3, 241-249 (2008)
"Ligand-stabilized hairpin structures interfere with elongation of human telomere."
M. Hagihara; Y. Goto; K. Nakatani
Chembiochem, 9, 510-513 (2008)
"Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides."
Y. Goto; A. Ohta; Y. Sako; Y. Yamagishi; H. Murakami; H. Suga
ACS Chem. Biol., 3, 120-129 (2008)
"Initiating translation with D-amino acids."
Y. Goto; H. Murakami; H. Suga
RNA, 14, 1390-1398 (2008)
"Analysis of mismatched DNA by mismatch binding ligand (MBL)-Sepharose affinity chromatography."
Y. Goto; H. Suda; A. Kobori; K. Nakatani
Anal. Bioanal. Chem., 388, 1165-1173 (2007)
"Small-molecule binding to the nonquadruplex form of the human telomeric sequence."
Y. Goto; S. Hagihara; M. Hagihara; K. Nakatani
Chembiochem, 8, 723-726 (2007)
"Evaluation of mismatch-binding ligands as inhibitors for Rev-RRE interaction."
K. Nakatani; S. Horie; Y. Goto; A. Kobori; S. Hagihara
Bioorg. Med. Chem., 14, 5384-5388 (2006)
"A new ligand binding to G-G mismatch having improved thermal and alkaline stability."
T. Peng; T. Murase; Y. Goto; A. Kobori; K. Nakatani
Bioorg. Med. Chem. Lett., 15, 259-262 (2005)
"Small-molecule ligand induces nucleotide flipping in (CAG)n trinucleotide repeats."
K. Nakatani; S. Hagihara; Y. Goto; A. Kobori; M. Hagihara; G. Hayashi; M. Kyo; M. Nomura; M. Mishima; C. Kojima
Nat. Chem. Biol., 1, 39-43 (2005)
"The binding of guanine-guanine mismatched DNA to naphthyridine dimer immobilized sensor surfaces: kinetic aspects."
K. Nakatani; A. Kobori; H. Kumasawa; Y. Goto; I. Saito
Bioorg. Med. Chem., 12, 3117-3123 (2004)
"Detection of guanine-adenine mismatches by surface plasmon resonance sensor carrying naphthyridine-azaquinolone hybrid on the surface."
S. Hagihara; H. Kumasawa; Y. Goto; G. Hayashi; A. Kobori; I. Saito; K. Nakatani
Nucleic Acids Res., 32, 278-286 (2004)

Publication (Books and reviews in Japanese)

"特殊ペプチド創薬 ー第三の創薬シーズの可能性を拓くー"
山田光博; 梅本詩織; 後藤佑樹; 菅裕明
現代化学, 4月号, 38-41 (2016)
西尾洸祐; 石橋正成; 後藤佑樹; 菅裕明
進化分子工学の最前線, 71-100 (2014)
"人工生合成系による化合物生産〜複雑な化合物を簡単に作る〜 ."
生命化学研究レター, 46, 4-9 (2014)
"アゾリン骨格含有ペプチドの試験管内生合成〜擬天然物の簡便・自在合成を目指して ."
化学と工業, 67, 707-708 (2014)
日本化学会バイオテクノロジー部会ニュースレター, 18, 11-13 (2014)
"In vitro synthetic biology of the genetic code: its development and applications."
H. Suga; C.J. Hipolito; Y. Goto; T. Katoh; N.K. Bashiruddin
Synthetic Biology, 1, 126-163 (2014)
東京大学新聞, 2643, 3 (2013)
ケミカルバイオロジー, (2013)
日本RNA学会会報, 28, 21-22 (2013)
後藤佑樹; 加藤敬行; 菅裕明
生命システム工学, 71-100 (2012)
伊藤悠美; 後藤佑樹; 菅裕明
最新ペプチド合成技術とその創薬研究への応用, 125-130 (2012)
後藤佑樹; 菅裕明
CSJカレントレビュー vol.6 核酸化学のニュートレンド, 32-35 (2011)
"A platform technology for the discovery of novel peptide drug leads, RaPID system"
Shimomai, D.; Goto, Y.; Suga, H.
Kagaku Kougyo, 2011, 62, 109-115.
"A new drug discovery strategy powered by RaPID system"
Goto, Y.; Ito, R.; Suga, H.
MEDCHEMNEWS, 2010, 20, 26-31.
生命科学研究レター, 33, (2010)
"Ribosomal synthesis of combinatorial polypeptides containing unusual amino acid blocks"
Goto, Y.; Ohta, A.; Murakami, H.; Suga, H. 
Kagaku Kougyo, 2007, 58, 255-262.


21 articles published in Peptide Science, Nucleic Acids Research Symposium Series, etc.