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
Associate professor, Graduate School of Science, The University of Tokyo

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)

"Post-translational backbone-acyl shift yields natural product-like peptides bearing hydroxyhydrocarbon units."
T. Kuroda; Y. Huang; S. Nishio; Y. Goto; H. Suga
Nature Chemistry, (2022)
"LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates."
Y.C. Zhang; K. Hamada; D.T. Nguyen; S. Inoue; M. Satake; S. Kobayashi; C. Okada; K. Ogata; M. Okada; T. Sengoku; Y. Goto; H. Suga
Nature Catalysis, 5, 682-+ (2022)
"De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors."
A.A. Vinogradov; Y. Zhang; K. Hamada; J.S. Chang; C. Okada; H. Nishimura; N. Terasaka; Y. Goto; K. Ogata; T. Sengoku; H. Onaka; H. Suga
J. Am. Chem. Soc., 144, 20332-20341 (2022)
"Solid-Phase-Based Synthesis of Lactazole-Like Thiopeptides."
Y. Zhang; A.A. Vinogradov; J.S. Chang; Y. Goto; H. Suga
Org. Lett., 24, 7894-7899 (2022)
"Accurate Models of Substrate Preferences of Post-Translational Modification Enzymes from a Combination of mRNA Display and Deep Learning."
A.A. Vinogradov; J.S. Chang; H. Onaka; Y. Goto; H. Suga
ACS Cent Sci, 8, 814-824 (2022)
"In Vitro Selection of Thioether-Closed Macrocyclic Peptide Ligands by Means of the RaPID System."
T. Katoh; Y. Goto; H. Suga
Methods Mol. Biol., 2371, 247-259 (2022)
"Site-Specific Nonenzymatic Peptide S/O-Glutamylation Reveals the Extent of Substrate Promiscuity in Glutamate Elimination Domains."
A.A. Vinogradov; M. Nagano; Y. Goto; H. Suga
J. Am. Chem. Soc., 143, 13358-13369 (2021)
"The RaPID Platform for the Discovery of Pseudo-Natural Macrocyclic Peptides."
Y. Goto; H. Suga
Acc Chem Res, 54, 3604-3617 (2021)
"Discovery and Development of Cyclic Peptide Inhibitors of CIB1."
V.A. Haberman; S.R. Fleming; T.M. Leisner; A.C. Puhl; E. Feng; L. Xie; X. Chen; Y. Goto; H. Suga; L.V. Parise; D. Kireev; K.H. Pearce; A.A. Bowers
ACS Med Chem Lett, 12, 1832-1839 (2021)
"Posttranslational chemical installation of azoles into translated peptides."
H. Tsutsumi; T. Kuroda; H. Kimura; Y. Goto; H. Suga
Nat. Commun., 12, 696 (2021)
"New developments in RiPP discovery, enzymology and engineering."
M. Montalban-Lopez; T.A. Scott; S. Ramesh; I.R. Rahman; A.J. van Heel; J.H. Viel; V. Bandarian; E. Dittmann; O. Genilloud; Y. Goto; M.J. Grande Burgos; C. Hill; S. Kim; J. Koehnke; J.A. Latham; A.J. Link; B. Martinez; S.K. Nair; Y. Nicolet; S. Rebuffat; H.G. Sahl; D. Sareen; E.W. Schmidt; L. Schmitt; K. Severinov; R.D. Sussmuth; A.W. Truman; H. Wang; J.K. Weng, et al.
Nat Prod Rep, 38, 130-239 (2021)
"Accurate Broadcasting of Substrate Fitness for Lactazole Biosynthetic Pathway from Reactivity-Profiling mRNA Display."
A.A. Vinogradov; E. Nagai; J.S. Chang; K. Narumi; H. Onaka; Y. Goto; H. Suga
J. Am. Chem. Soc., 142, 20329-20334 (2020)
"Human trans-editing enzyme displays tRNA acceptor-stem specificity and relaxed amino acid selectivity."
O. Vargas-Rodriguez; M. Bakhtina; D. McGowan; J. Abid; Y. Goto; H. Suga; K. Musier-Forsyth
J. Biol. Chem., 295, 16180-16190 (2020)
"Promiscuous Enzymes Cooperate at the Substrate Level En Route to Lactazole A."
A.A. Vinogradov; M. Shimomura; N. Kano; Y. Goto; H. Onaka; H. Suga
J. Am. Chem. Soc., 142, 13886-13897 (2020)
"A Macrocyclic Peptide Library with a Structurally Constrained Cyclopropane-containing Building Block Leads to Thiol-independent Inhibitors of Phosphoglycerate Mutase."
R. Okuma; T. Kuwahara; T. Yoshikane; M. Watanabe; P. Dranchak; J. Inglese; S. Shuto; Y. Goto; H. Suga
Chem. Asian J., 15, 2631-2636 (2020)
"Minimal lactazole scaffold for in vitro thiopeptide bioengineering."
A.A. Vinogradov; M. Shimomura; Y. Goto; T. Ozaki; S. Asamizu; Y. Sugai; H. Suga; H. Onaka
Nat. Commun., 11, 2272 (2020)
"Chemoenzymatic Posttranslational Modification Reactions for the Synthesis of Ψ[CH2NH]-Containing Peptides."
Y. Kato; T. Kuroda; Y. Huang; R. Ohta; Y. Goto; H. Suga
Angew. Chem. Int. Ed. Engl., 59, 684-688 (2020)
"In Vitro Biosynthesis of Peptides Containing Exotic Azoline Analogues."
Y. Goto; H. Suga
ChemBioChem, 21, 84-87 (2020)
"Exploring the Post-translational Enzymology of PaaA by mRNA Display."
S.R. Fleming; P.M. Himes; S.V. Ghodge; Y. Goto; H. Suga; A.A. Bowers
J. Am. Chem. Soc., 142, 5024-5028 (2020)
"Improved Stability of siRNA-Loaded Lipid Nanoparticles Prepared with a PEG-Monoacyl Fatty Acid Facilitates Ligand-Mediated siRNA Delivery."
Y. Sakurai; W. Mizumura; K. Ito; K. Iwasaki; T. Katoh; Y. Goto; H. Suga; H. Harashima
Mol. Pharm., 17, 1397-1404 (2020)
"Generation of non-standard macrocyclic peptides specifically binding TSC-22 homologous gene-1."
S.T.P. Tran; C.J. Hipolito; H. Suzuki; R. Xie; H.D. Kim Tuyen; P.T. Dijke; N. Terasaka; Y. Goto; H. Suga; M. Kato
Biochem. Biophys. Res. Commun., 516, 445-450 (2019)
"Ribosomal Synthesis of Backbone-Cyclic Peptides Compatible with In Vitro Display."
R. Takatsuji; K. Shinbara; T. Katoh; Y. Goto; T. Passioura; R. Yajima; Y. Komatsu; H. Suga
J. Am. Chem. Soc., 141, 2279-2287 (2019)
"Ribosomal Formation of Thioamide Bonds in Polypeptide Synthesis."
R. Maini; H. Kimura; R. Takatsuji; T. Katoh; Y. Goto; H. Suga
J. Am. Chem. Soc., 141, 20004-20008 (2019)
"Meeting Peptides in Kyoto."
S. Futaki; K. Matsuzaki; Y. Goto
Chembiochem, 20, 2015-2016 (2019)
"Flexizyme-Enabled Benchtop Biosynthesis of Thiopeptides."
S.R. Fleming; T.E. Bartges; A.A. Vinogradov; C.L. Kirkpatrick; Y. Goto; H. Suga; L.M. Hicks; A.A. Bowers
J. Am. Chem. Soc., 141, 758-762 (2019)
"Non-competitive cyclic peptides for targeting enzyme-substrate complexes."
T.E. McAllister; T.L. Yeh; M.I. Abboud; I.K.H. Leung; E.S. Hookway; O.N.F. King; B. Bhushan; S.T. Williams; R.J. Hopkinson; M. Munzel; N.D. Loik; R. Chowdhury; U. Oppermann; T.D.W. Claridge; Y. Goto; H. Suga; C.J. Schofield; A. Kawamura
Chem Sci, 9, 4569-4578 (2018)
"Engineering of RiPP pathways for the production of artificial peptides bearing various non-proteinogenic structures."
Y. Goto; H. Suga
Curr. Opin. Chem. Biol., 46, 82-90 (2018)
"Artificial In Vitro Biosynthesis Systems for the Development of Pseudo-Natural Products."
Y. Goto; H. Suga
Bull Chem Soc Jpn, 91, 410-419 (2018)
"Artificial Division of Codon Boxes for Expansion of the Amino Acid Repertoire of Ribosomal Polypeptide Synthesis."
Y. Iwane; T. Katoh; Y. Goto; H. Suga
Methods Mol Biol, 1728, 17-47 (2018)
"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)
"Efficient siRNA Delivery by Lipid Nanoparticles Modified with a Nonstandard Macrocyclic Peptide for EpCAM-Targeting."
Y. Sakurai; W. Mizumura; M. Murata; T. Hada; S. Yamamoto; K. Ito; K. Iwasaki; T. Katoh; Y. Goto; A. Takagi; M. Kohara; H. Suga; H. Harashima
Mol Pharm, 14, 3290-3298 (2017)
"Conformational and chemical selection by a trans-acting editing domain."
E.M. Danhart; M. Bakhtina; W.A. Cantara; A.B. Kuzmishin; X. Ma; B.L. Sanford; M. Kosutic; Y. Goto; H. Suga; K. Nakanishi; R. Micura; M.P. Foster; K. Musier-Forsyth
Proc. Natl. Acad. Sci. USA, 114, E6774-E6783 (2017)
"Quality control by trans-editing factor prevents global mistranslation of non-protein amino acid alpha-aminobutyrate."
J.M. Bacusmo; A.B. Kuzmishin; W.A. Cantara; Y. Goto; H. Suga; K. Musier-Forsyth
RNA Biol, 0 (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)
"A Post-translational Cyclodehydratase, PatD, Tolerates Sequence Variation in the C-terminal Region of Substrate Peptides."
Y. Goto; H. Suga
Chem Lett, 45, 1247-1249 (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)

36 Japanese articles/books have been published.


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