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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. 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 2024; 14:798. [PMID: 39062512 PMCID: PMC11275124 DOI: 10.3390/biom14070798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
Enzymatic transglycosylation of the fleximer base 4-(4-aminopyridine-3-yl)-1H-pyrazole using recombinant E. coli purine nucleoside phosphorylase (PNP) resulted in the formation of "non-typical" minor products of the reaction. In addition to "typical" N1-pyrazole nucleosides, a 4-imino-pyridinium riboside and a N1-pyridinium-N1-pyrazole bis-ribose derivative were formed. N1-Pyrazole 2'-deoxyribonucleosides and a N1-pyridinium-N1-pyrazole bis-2'-deoxyriboside were formed. But 4-imino-pyridinium deoxyriboside was not formed in the reaction mixture. The role of thermodynamic parameters of key intermediates in the formation of reaction products was elucidated. To determine the mechanism of binding and activation of heterocyclic substrates in the E. coli PNP active site, molecular modeling of the fleximer base and reaction products in the enzyme active site was carried out. As for N1-pyridinium riboside, there are two possible locations for it in the PNP active site. The presence of a relatively large space in the area of amino acid residues Phe159, Val178, and Asp204 allows the ribose residue to fit into that space, and the heterocyclic base can occupy a position that is suitable for subsequent glycosylation. Perhaps it is this "upside down" arrangement that promotes secondary glycosylation and the formation of minor bis-riboside products.
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Affiliation(s)
- Barbara Z. Eletskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Anton F. Mironov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
- Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia Named after Patrice Lumumba, Miklukho-Maklaya St. 6, Moscow 117198, Russia
| | - Ilya V. Fateev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Maria Ya. Berzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Konstantin V. Antonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Olga S. Smirnova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexandra B. Zatsepina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexandra O. Arnautova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Yulia A. Abramchik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexander S. Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexey L. Kayushin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Anastasia L. Khandazhinskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Elena S. Matyugina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Sergey N. Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Anatoly I. Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Igor A. Mikhailopulo
- Institute of Bioorganic Chemistry, National Academy of Sciences, Acad. Kuprevicha 5/2, 220141 Minsk, Belarus;
| | - Roman S. Esipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Irina D. Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
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