"De Novo Discovery of Pseudo-Natural Prenylated Macrocyclic Peptide Ligands"

S. Inoue; D. Thanh Nguyen; K. Hamada; R. Okuma; C. Okada; M. Okada; I. Abe; T. Sengoku; Y. Goto; H. Suga

Angew. Chem. Int. Ed. Engl., 63, e202409973 (2024)

"Oxidation-guided and collision-induced linearization assists de novo sequencing of thioether macrocyclic peptides"

A. Hayashi; Y. Goto; Y. Saito; H. Suga; J. Morimoto; S. Sando

Chem. Commun., 60, 9436-9439 (2024)

"A Compact Reprogrammed Genetic Code for De Novo Discovery of Proteolytically Stable Thiopeptides"

A.A. Vinogradov; Y. Zhang; K. Hamada; S. Kobayashi; K. Ogata; T. Sengoku; Y. Goto; H. Suga

J. Am. Chem. Soc., 146, 8058-8070 (2024)

"Modulating the Acceptor Preference of His-C-Geranyltransferase LimF"

Y.C. Zhang; Y. Goto; H. Suga

Isr. J. Chem., 64, (2024)

"Switching Prenyl Donor Specificities of Cyanobactin Prenyltransferases"

Y. Zhang; K. Hamada; M. Satake; T. Sengoku; Y. Goto; H. Suga

J. Am. Chem. Soc., 145, 23893-23898 (2023)

"Deep Learning-Driven Library Design for the De Novo Discovery of Bioactive Thiopeptides"

J.S. Chang; A.A. Vinogradov; Y. Zhang; Y. Goto; H. Suga

ACS Cent. Sci., 9, 2150-2160 (2023)

"Discovery, biochemical characterization, and bioengineering of cyanobactin prenyltransferases"

Y. Zhang; Y. Goto; H. Suga

Trends Biochem. Sci., 48, 360-374 (2023)

"Label-free quantification of passive membrane permeability of cyclic peptides across lipid bilayers: penetration speed of cyclosporin A across lipid bilayers"

T. Ono; K.V. Tabata; Y. Goto; Y. Saito; H. Suga; H. Noji; J. Morimoto; S. Sando

Chem. Sci., 14, 345-349 (2023)

"Structural basis of tRNAPro acceptor stem recognition by a bacterial trans-editing domain"

X. Ma; M. Bakhtina; I. Shulgina; W.A. Cantara; A.B. Kuzmishin Nagy; Y. Goto; H. Suga; M.P. Foster; K. Musier-Forsyth

Nucleic Acids Res., 51, 3988-3999 (2023)

"Ribosomal Synthesis of Peptides Bearing Noncanonical Backbone Structures via Chemical Posttranslational Modifications"

Y. Goto; H. Suga

Methods Mol. Biol., 2670, 255-266 (2023)

"Reactivity and mechanism in chemical and synthetic biology"

N.G.J. Richards; S.L. Bearne; Y. Goto; E.J. Parker

Phil. Trans. B, 378, (2023)

"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

Nat. Catal., 5, 682-+ (2022)

"Post-translational backbone-acyl shift yields natural product-like peptides bearing hydroxyhydrocarbon units"

T. Kuroda; Y. Huang; S. Nishio; Y. Goto; H. Suga

Nat. Chem., 14, 1413-1420 (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)

"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)

"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)

"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)

"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)

"The RaPID platform for the discovery of pseudo-natural macrocyclic peptides"

Y. Goto; H. Suga

Acc. Chem. Res., 54, 3604-3617 (2021)

"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)

"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)

"Mid-sized macrocyclic peptides as a new drug modality"

Y. Goto; N. M.; H. Suga

In Middle Molecular Strategy (Springer), pp. 97-107 (2021)

"Development of flexizyme aminoacylation ribozymes, and their applications"

T. Katoh; Y. Goto; T. Passioura; H. Suga

In Ribozymes: Principles, Methods, Applications, S. Müller, B. Masquida, and W. Winkler, eds. (Wiley), pp. 519-543 (2021)

"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)

"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)

"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)

"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)

"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)

"Chemoenzymatic posttranslational modification reactions for the synthesis of psi[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)

"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)

"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)

"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)

"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., 15, 576-585 (2018)

"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)

"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

Nat. Commun., 8, 14207 (2017)

"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

Nat. Commun., 8, 14773 (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)

"Biological synthesis and affinity-based selection of small macrocyclic peptide ligands"

T. Passioura; T. Katoh; Y. Goto; H. Suga

In Cyclic Peptides: From Bioorganic Synthesis to Applications, J. Koehnke, J. Naismith, and W.A.v.d. Donk, eds. (RSC Publishing), pp. 225-254 (2017)

"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

Nat. Chem., 8, 317-325 (2016)

"A posttranslational cyclodehydratase, PatD, tolerates sequence variation in the C-terminal region of the substrate peptides"

Y. Goto; H. Suga

Chem. Lett., 45, 1247-1249 (2016)

"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)

"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)

"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

Int. J. Mol. Sci., 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

J. Biol. Chem., 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

Curr. Opin. Chem. Biol., 26C, 34-41 (2015)

"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

Proc. Natl. Acad. Sci. USA, 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

J. Mol. Evol., 81, 210-217 (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)

"In vitro synthetic biology of the genetic code: its development and applications"

H. Suga; C.J. Hipolito; Y. Goto; T. Katoh; N.K. Bashiruddin

In Synthetic Biology, M. Ryadnov, L. Brunsveld, and H. Suga, eds. (RSC Publishing), pp. 126-163 (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)