Publications

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Primary research articles

34. Y. Zhang, A. Vinogradov, and H. Suga.^‡ Ribosomal Synthesis of Topologically Defined Thioisoindole-Bridged Bicyclic Peptides. Angew. Chem. Int. Ed. 2025, e17689
    
    
35. D. Nguyen, J. Ramos-Figueroa, A. Vinogradov, Y. Goto, M. Gadgil, R. Splain, H. Suga, W. van der Donk,^‡ and D. Mitchell^‡. Aminoacyl-tRNA specificity of a ligase catalyzing non-ribosomal peptide extension. J. Am. Chem. Soc. 2025, 147, 37893–37898.
    
    
36. A. Vinogradov^‡ and H. Suga^‡. Measuring k_cat/K_M values for over 200,000 enzymatic substrates with mRNA display. Chem, 2026, 12, 102737
    
37. A. Vinogradov^‡, S. Pan, and H. Suga^‡. Ligand-enabled selective coupling of MIDA boronates to dehydroalanine-containing peptides and proteins. J. Am. Chem. Soc. 2025, 147, 7533–7544
    
    
38. A. Vinogradov,^‡ G. Bashiri, and H. Suga^‡. Illuminating substrate preferences of promiscuous F₄₂₀H₂-dependent dehydroamino acid reductases with 4-track messenger RNA display. J. Am. Chem. Soc. 2024, 146, 31124–31136.
    
    
39. Y. Ohno, A. Vinogradov,^‡ and H. Suga^‡. Selective pH-responsive conjugation between a pair of de novo discovered peptides. J. Am. Chem. Soc. 2024, 146, 29429–29440.
    
    
40. H. King, M. Bycroft, T. Nguyen, G. Kelly, A .Vinogradov, P. Rowling, K. Stott, D. Ascher, H. Suga, L. Itzhaki, K. Artavanis-Tsakonas^‡. Targeting the Plasmodium falciparum UCHL3 ubiquitin hydrolase using chemically constrained peptides. Proc. Natl. Acad. Sci. U. S. A., 2024, 121, e2322923121.
    
    
41. A. Vinogradov,^†,‡ Y. Zhang,^† K. Hamada, S. Kobayashi, K. Ogata, T. Sengoku, Y. Goto,^‡ and H. Suga^‡. A Compact Reprogrammed Genetic Code for de Novo Discovery of Proteolytically Stable Thiopeptides. J. Am. Chem. Soc. 2024, 146, 8058−8070.
    
    
42. J. Chang, A. Vinogradov,^‡ Y. Zhang, Y. Goto,^‡ and H. Suga.^‡ Deep Learning-Driven Library Design for the De Novo Discovery of Bioactive Thiopeptides. ACS Cent. Sci. 2023, 9, 2150−2160.
    
    
43. A. Vinogradov, Y. Zhang, K. Hamada, J. Chang, C. Okada, H. Nishimura, N. Terasaka, Y. Goto,^‡ K. Ogata, T. Sengoku, H. Onaka, and H. Suga.^‡ De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors. J. Am. Chem. Soc. 2022, 144, 20332−20341.
    
    
44. Y. Zhang, A. Vinogradov,^‡ J. Chang, Y. Goto, and H. Suga.^‡ Solid-Phase-Based Synthesis of Lactazole-Like Thiopeptides. Org. Lett. 2022, 24, 7894−7899.
    
    
45. A. Vinogradov,^‡ J. Chang, H. Onaka, Y. Goto, and H. Suga.^‡ Accurate Models of Substrate Preferences of Post-Translational Modification Enzymes from a Combination of mRNA Display and Deep Learning. ACS Cent. Sci. 2022, 8, 814−824.
    
    
46. A. Vinogradov,^‡ M. Nagano, Y. Goto, and H. Suga.^‡ Site-Specific Nonenzymatic Peptide S/O-Glutamylation Reveals the Extent of Substrate Promiscuity in Glutamate Elimination Domains. J. Am. Chem. Soc. 2021, 143, 13358–13369.
    
    
47. A. Vinogradov,^‡ E. Nagai, J. Chang, K. Narumi, H. Onaka,^‡ Y. Goto,^‡ and H. Suga.^‡ Accurate Broadcasting of Substrate Fitness for Lactazole Biosynthetic Pathway from Reactivity-Profiling mRNA Display. J. Am. Chem. Soc. 2020, 142, 20329−20334.
    
48. A. Vinogradov, M. Shimomura, N. Kano, Y. Goto, H. Onaka, and H. Suga. ^‡ Promiscuous Enzymes Cooperate at the Substrate Level En Route to Lactazole A. J. Am. Chem. Soc. 2020, 142, 13886–13897.
    
    
49. A. Vinogradov,^† M. Shimomura,^† Y. Goto,^‡ T. Ozaki, S. Asamizu, Y. Sugai, H. Suga,^‡ and H. Onaka.^‡ Minimal lactazole scaffold for in vitro thiopeptide bioengineering. Nat. Commun. 2020, 11, 2272.
    
    
50. O. Bondarenko,^‡ A. Vinogradov, A. Komarov, G. Karetnikov, N. Zyk, T. Holt, and A. Kutateladze. Access to 5-fluoroisoxazoles via the nitrosation of geminal bromo-fluoro arylcyclopropanes. Tetrahedron. 2019, 75, 2861–2865.
    
    
51. S. Fleming, T. Bartges, A. Vinogradov, C. Kirkpatrick, Y. Goto, H. Suga,  L. Hicks, and A. Bowers.^‡ Flexizyme-Enabled Benchtop Biosynthesis of Thiopeptides. J. Am. Chem. Soc., 2019, 141, 758–762.
    
    
52. Z. Gates,^‡ A. Vinogradov, A. Quartararo, A. Bandyopadhyay, Z.-N. Choo, E. Evans, K. Halloran, A. Mijalis, S. Mong, M. Simon, E. Standley, E. Styduhar, S. Tasker, F. Touti, J. Weber, J. Wilson, T. Jamison, and B. Pentelute.^‡ Xenoprotein engineering via synthetic libraries. Proc. Natl. Acad. Sci. U. S. A., 2018, 115, E5298–E5306.
    
    
53. C. Zhang, P. Dai, A. Vinogradov, Z. Gates, and B. Pentelute.^‡ Site-Selective Cysteine–Cyclooctyne Conjugation. Angew. Chem. Int. Ed. 2018, 57, 6459–6463.
    
    
54. A. Vinogradov,^‡ Z. Gates, C. Zhang, A. Quartararo, K. Halloran, and B. Pentelute.^‡ Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries. ACS Comb. Sci. 2017, 19, 694−701.
    
    
55. M. Simon, Y. Maki, A. Vinogradov, C. Zhang, H. Yu, Y.-S. Lin, Y. Kajihara, and B. Pentelute.^‡ D-amino acid scan of two small proteins. J. Am. Chem. Soc., 2016, 138, 12099−12111.
    
    
56. A. Vinogradov, Z.-N. Choo, K. Totaro, and B. Pentelute.^‡ Macrocyclization of Unprotected Peptide Isocyanates. Org. Lett. 2016, 18, 1226–1229.
    
    
57. A. Vinogradov, M. Simon, and B. Pentelute.^‡ C‑Terminal Modification of Fully Unprotected Peptide Hydrazides via in Situ Generation of Isocyanates. Org. Lett. 2016, 18, 1222–1225.
    
    
58. O. Bondarenko,^‡ A. Vinogradov, A. Komarov, A. Smirnov, and N. Zyk. Synthesis of 5-fluoro- and 5-bromoalkylisoxazoles via nitrosation of 1,1-dihalocyclopropanes with sulfur trioxide activated nitrosyl chloride. J. Fluor. Chem. 2016, 185, 201–205.
    
    
59. A. Vinogradov, E. Evans, and B. Pentelute.^‡ Total synthesis and biochemical characterization of mirror image barnase. Chem. Sci. 2015, 6, 2997–3002.
    
    
60. O. Bondarenko,^‡ A. Vinogradov, P. Danilov, S. Nikolaeva, A. Gavrilova, and N. Zyk. Nitrosation of 2-aryl-1,1-dibromocyclopropanes: synthesis of 3-aryl-5-bromoisoxazoles. Tetrahedron Lett. 2015, 56, 6577–6579.
    
    
61. S. Mong,^† A. Vinogradov,^† M. Simon, and B. Pentelute.^‡ Rapid Total Synthesis of DARPin pE59 and Barnase. ChemBioChem 2014, 15, 721–733.
    
    
62. M. Simon, P. Heider, A. Adamo, A. Vinogradov, S. Mong, X. Li, T. Berger, R. Policarpo, C. Zhang, Y. Zou, X. Liao, A. Spokoyny, K. Jensen, and B. Pentelute.^‡ Rapid Flow-Based Peptide Synthesis. ChemBioChem 2014, 15, 713–720.
    
    
63. V. Prituzhalov, E. Ardashnikova,^‡ A. Vinogradov, V. Dolgikh, J.-J. Videau, E. Fargin, A. Abakumov, N. Tarakina, and G. Van Tendeloo. New anion-conducting solid solutions Bi_1−xTex(O,F)_2+δ (x > 0.5) and glass–ceramic materials on their base. J. Fluor. Chem. 2011, 132, 1110–1116.
    

Reviews

4. A. Vinogradov^‡ and H. Suga.^‡ Introduction to Thiopeptides: Biological Activity, Biosynthesis, and Strategies for Functional Reprogramming. Cell Chem. Biol. 2020, 27, 1032–1051.
   
5. A. Vinogradov, Y. Yin, and H. Suga.^‡ Macrocyclic Peptides as Drug Candidates: Recent Progress and Remaining Challenges. J. Am. Chem. Soc. 2019, 141, 4167–4181.
   

Book chapters

2. M. Simon, A. Mijalis, K. Totaro, D. Dunkelmann, A. Vinogradov, C. Zhang, Y. Maki, J. Wolfe, J. Wilson, A. Loas, and B. Pentelute.^‡ Automated Fast Flow Peptide Synthesis, in Total Chemical Synthesis of Proteins, John Wiley & Sons, 2021, 17–58.
   Link to chapter
   
3. R. van Neer, A. Vinogradov, and H. Suga.^‡ RaPID Discovery of Macrocyclic Peptide Inhibitors of Protein–Protein Interactions, in Inhibitors of Protein–Protein Interactions, Royal Society of Chemistry, 2020, 232–246.
   Link to chapter