Enzymatic systems for the synthesis of pharmaceutically significant modified nucleosides and nucleotides as an object for rational optimization

Modified nucleosides constitute a large group of synthetic drugs. Cladribine, nelarabine, fludarabine, cytarabine are widely used for the treatment of oncohematological diseases; for viral infections - azidothymidine, maribavir, ribavirin, vidarabine, sofosbuvir. Their production is facilitated by the development of an integrated chemico-enzymatic synthesis approach using recombinant nucleic acid exchange enzymes. Within the framework of this project, it is planned to synthesize new potential anticancer drugs: N6-purine-substituted analogues of Clofarabine, an inhibitor of ribonucleotide reductase and DNA polymerase, which is used in the treatment of acute lymphoblastic leukemia, as well as to carry out glycosylation of a purine conjugate with benzoxazine, which has a high cytotoxic activity, where as a linker the 11-aminoundecanoic acid residue is used. It is planned to expand the series of 3-substituted analogues of ribavirin, a synthetic nucleoside used in the treatment of hepatitis C. Using biosynthesis, a series of new ribo- and 2'-deoxyribosides of 1,2,4-triazole with hydrophobic substituents in the C3 position will be obtained. We have shown that 2-fluorocordycepine has antiproliferative activity, but the biosynthesis of this drug using recombinant E. coli purine nucleoside phosphorylase (PNP) occurs with low yield. This project proposes to consider two potential solutions: a) studying the possibility of using 3'-deoxyuridine in biosynthesis; b) rational design of the active site of nucleoside phosphorylases (NPs), aimed at increasing the affinity for the enzyme. The substrate specificity of PNP does not allow the production of antiviral (phospho)ribosylated derivatives of pyrazine-2-carboxamide, in particular, the substance T-705, an antiviral purine mimetic prodrug known as “favipiravir” (“avifavir”), which is used in the treatment of various viral infections, including COVID-19. The active substance is T-705-riboside-5'-triphosphate, which is formed in vivo, but the low efficiency of drug activation by phosphoribosylation requires a very high dose load. The experience of our research (including those supported by the Russian Science Foundation) has shown that the problem of phosphoribosylated derivatives of the prodrug T-705 synthesis can be solved using rational enzyme design. We plan to utilize and expand this approach to design mutant forms of recombinant nucleoside phosphorylases. Using the engineered mutants, we plan to carry out the biosynthesis of antiviral favipiravir derivatives. Previously, our group has developed mono- and polyenzymatic cascades intended for the production of antiviral and antitumor drugs. Our planned studies are aimed at optimizing these systems through the rational design of enzyme active sites. The results of such studies will make it possible to overcome the limitations of the natural substrate specificity of enzymes and simplify technologies for the production of pharmaceutically significant compounds. The goal of this project is to develop at a new level a chemical-enzymatic approach to the synthesis of new modified nucleosides and nucleotides to obtain a series of compounds with unnatural heterocyclic bases and carbohydrate fragments and to study their antitumor and antiviral activity in in vitro experiments. Due to the wide variety of targets that the new compound can act on, this project involves screening for antiviral and antitumor activity of all obtained substances. The results obtained within the framework of the project will include not only new active modified nucleosides and nucleotides, but also preparations of recombinant enzymes with modified substrate characteristics, which contributes to the fulfillment of the global goal of the project - the targeted creation of new drugs for the treatment of socially significant human diseases in accordance with the approaches “green chemistry”.

December 6, 2023 — December 31, 2026

Esipov R.S. (PI)

Laboratory of Biopharmaceutical Technologies

Grant, RSF

List of publications

  1. Eletskaya BZ, Mironov AF, Fateev IV, Berzina MY, Antonov KV, Smirnova OS, Zatsepina AB, Arnautova AO, Abramchik YA, Paramonov AS, Kayushin AL, Khandazhinskaya AL, Matyugina ES, Kochetkov SN, Miroshnikov AI, Mikhailopulo IA, Esipov RS, Konstantinova ID (2024). Enzymatic Transglycosylation Features in Synthesis of 8-Aza-7-Deazapurine Fleximer Nucleosides by Recombinant E. coli PNP: Synthesis and Structure Determination of Minor Products. Biomolecules 14 (7), 798
  2. Fateev IV, Sasmakov SA, Abdurakhmanov JM, Ziyaev AA, Khasanov SS, Eshboev FB, Ashirov ON, Frolova VD, Eletskaya BZ, Smirnova OS, Berzina MY, Arnautova AO, Abramchik YA, Kostromina MA, Kayushin AL, Antonov KV, Paramonov AS, Andronova VL, Galegov GA, Esipov RS, Azimova SS, Miroshnikov AI, Konstantinova ID (2024). Synthesis of Substituted 1,2,4-Triazole-3-Thione Nucleosides Using E. coli Purine Nucleoside Phosphorylase. Biomolecules 14 (7), 745
  3. Fateev IV, Sasmakov SA, Ziyaev AA, Abdurakhmanov ZM, Toshmurodov TT, Ikramov SA, Tosheva NA, Frolova VD, Zorina EA, Zayats EA, Eletskaya BZ, Smirnova OS, Berzina MY, Arnautova AO, Abramchik YA, Kostromina MA, Kayushin AL, Antonov KV, Prokhorenko IA, Paramonov AS, Аndronova VL, Esipov RS, Azimova SS, Miroshnikov AI, Konstantinova ID (2025). Enzymatic Synthesis and Molecular Docking Studies of Substituted 5-Phenyl-1,2,4-triazole-3-thione Deoxyribosides. Russ. J. Bioorganic Chem. 51 (4), 1780–1788
  4. Zayats EA, Abramchik YA, Kostromina MA, Timofeev VI, Shevtsov MB, Mishin AV, Fateev IV, Karanov AA, Sharafutdinova AR, Arnautova AO, Konstantinova ID, Borshchevskiy VI, Esipov RS (2025). Interference of Sulphonate Buffering Agents with E. coli Hypoxanthine-Guanine Phosphoribosyltransferase Active Site Functioning: A Crystallographic and Enzymological Study. Crystals (Basel) 15 (10), 874
  5. Arnautova AO, Aleksakhina IA, Zorina EA, Berzina MY, Fateev IV, Eletskaya BZ, Antonov KV, Smirnova OS, Paramonov AS, Kayushin AL, Andronova VL, Galegov GA, Kostromina MA, Zayats EA, Karpenko IL, Kotovskaya SK, Charushin VN, Esipov RS, Miroshnikov AI, Konstantinova ID (2025). New Benzimidazole 3′-Deoxynucleosides: Synthesis and Antiherpes Virus Properties. Biomolecules 15 (7), 922
  6. Zayats EA, Abramchik YA, Kostromina MA, Konstantinova ID, Esipov RS (2026). Mutant Forms of Nucleoside Phosphorylases and Other Nucleic Acid Metabolism Enzymes for the Optimization of Cascade Synthesis of Modified Nucleosides. Russ. J. Bioorganic Chem. 52 (4), 100
  7. Mironov AF, Eletskaya BZ, Antonov KV, Paramonov AS, Esipov RS, Konstantinova ID, Andreevskaya SN, Smirnova TG, Karpenko IL, Sokhraneva VA, Zhivotova IS, Kochetkov SN, Khandazhinskaya AL, Matyugina ES (2026). Exploring Novel Indazole and Pyrazole Nucleoside Analogues: Enzymatic Synthesis, Characterization, and Biological Evaluation. Int J Mol Sci 27 (17), 7551
  8. Zayats EA, Abramchik YA, Kostromina MA, Fateev IV, Karanov AA, Sharafutdinova AR, Ptushkin VA, Konstantinova ID, Golovin AV, Esipov RS (2026). Enhancing the Activity of Ribokinase from Thermus sp. 2.9 Through Rational Design for the Cascade Synthesis of Modified Nucleotides and Nucleosides. Int J Mol Sci 27 (19), 8911