Effect of 8-Oxo-1,N⁶-Ethenoadenine Derivatives on the Activity of RNA Polymerases from SARS-CoV-2 and Escherichia coli

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Ivan V. Petushkov^1,2,a#, Andrey V. Aralov^3,4#, Igor A. Ivanov^3,5, Mikhail S. Baranov^3,6, Timofey S. Zatsepin⁷, Andrey V. Kulbachinskiy^1,2,b*

¹National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia

²Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia

³Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia

⁴RUDN University, 117198 Moscow, Russia

⁵Organicum LLC, 127486 Moscow, Russia

⁶Pirogov Russian National Research Medical University, 117997 Moscow, Russia

⁷Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia

^* To whom correspondence should be addressed.

^# These authors contributed equally to the work.

Received: October 26, 2024; Revised: November 29, 2024; Accepted: December 1, 2024

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Bacterial and viral RNA polymerases are promising targets for the development of new transcription inhibitors. One of the potential blockers of RNA synthesis is 7,8-dihydro-8-oxo-1,N⁶-ethenoadenine (oxo-εA), a synthetic compound that combines two adenine modifications: 8-oxoadenine and 1,N⁶-ethenoadenine. In this study, we synthesized oxo-εA triphosphate (oxo-εATP) and showed that it could be incorporated by the RNA-dependent RNA polymerase of SARS-CoV-2 into synthesized RNA opposite template residues A and G in the presence of Mn²⁺ ions. Escherichia coli RNA polymerase incorporated oxo-εATP opposite A residues in the template DNA strand. The presence of oxo-εA instead of adenine in the template DNA strand completely stopped transcription at the modified nucleotide. At the same time, oxo-εATP did not suppress RNA synthesis by both RNA polymerases in the presence of unmodified nucleotides. Therefore, the oxo-εA modification significantly disrupts nucleotide base pairing during RNA synthesis by RNA polymerases of different classes, and the corresponding nucleotide derivatives cannot be used as potential antiviral or antibacterial transcription inhibitors.

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KEY WORDS: modified nucleobases, RNA polymerase, transcription, transcription inhibitors, SARS-CoV-2

DOI: 10.1134/S0006297924120149

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