Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2′-Deoxyzebularine Analogues

Maksim V. Kvach, Fareeda M. Barzak, Stefan Harjes, Henry A.M. Schares, Geoffrey B. Jameson, Alex M. Ayoub, Ramkumar Moorthy, Hideki Aihara, Reuben Harris, Vyacheslav V. Filichev, Daniel A Harki, Elena Harjes

Research output: Contribution to journalArticle

Abstract

APOBEC3 enzymes form part of the innate immune system by deaminating cytosine to uracil in single-stranded DNA (ssDNA) and thereby preventing the spread of pathogenic genetic information. However, APOBEC mutagenesis is also exploited by viruses and cancer cells to increase rates of evolution, escape adaptive immune responses, and resist drugs. This raises the possibility of APOBEC3 inhibition as a strategy for augmenting existing antiviral and anticancer therapies. Here we show that, upon incorporation into short ssDNAs, the cytidine nucleoside analogue 2′-deoxyzebularine (dZ) becomes capable of inhibiting the catalytic activity of selected APOBEC variants derived from APOBEC3A, APOBEC3B, and APOBEC3G, supporting a mechanism in which ssDNA delivers dZ to the active site. Multiple experimental approaches, including isothermal titration calorimetry, fluorescence polarization, protein thermal shift, and nuclear magnetic resonance spectroscopy assays, demonstrate nanomolar dissociation constants and low micromolar inhibition constants. These dZ-containing ssDNAs constitute the first substrate-like APOBEC3 inhibitors and, together, comprise a platform for developing nucleic acid-based inhibitors with cellular activity.

Original languageEnglish (US)
Pages (from-to)391-400
Number of pages10
JournalBiochemistry
Volume58
Issue number5
DOIs
StatePublished - Feb 5 2019

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Single-Stranded DNA
Cytidine
Mutagenesis
Calorimetry
Fluorescence Polarization
Uracil
Immune system
Cytosine
Adaptive Immunity
Titration
Viruses
Nucleosides
Nucleic Acids
Nuclear magnetic resonance spectroscopy
Antiviral Agents
Immune System
Assays
Catalyst activity
Catalytic Domain
Magnetic Resonance Spectroscopy

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

Cite this

Kvach, M. V., Barzak, F. M., Harjes, S., Schares, H. A. M., Jameson, G. B., Ayoub, A. M., ... Harjes, E. (2019). Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2′-Deoxyzebularine Analogues. Biochemistry, 58(5), 391-400. https://doi.org/10.1021/acs.biochem.8b00858

Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2′-Deoxyzebularine Analogues. / Kvach, Maksim V.; Barzak, Fareeda M.; Harjes, Stefan; Schares, Henry A.M.; Jameson, Geoffrey B.; Ayoub, Alex M.; Moorthy, Ramkumar; Aihara, Hideki; Harris, Reuben; Filichev, Vyacheslav V.; Harki, Daniel A; Harjes, Elena.

In: Biochemistry, Vol. 58, No. 5, 05.02.2019, p. 391-400.

Research output: Contribution to journalArticle

Kvach, MV, Barzak, FM, Harjes, S, Schares, HAM, Jameson, GB, Ayoub, AM, Moorthy, R, Aihara, H, Harris, R, Filichev, VV, Harki, DA & Harjes, E 2019, 'Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2′-Deoxyzebularine Analogues', Biochemistry, vol. 58, no. 5, pp. 391-400. https://doi.org/10.1021/acs.biochem.8b00858
Kvach MV, Barzak FM, Harjes S, Schares HAM, Jameson GB, Ayoub AM et al. Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2′-Deoxyzebularine Analogues. Biochemistry. 2019 Feb 5;58(5):391-400. https://doi.org/10.1021/acs.biochem.8b00858
Kvach, Maksim V. ; Barzak, Fareeda M. ; Harjes, Stefan ; Schares, Henry A.M. ; Jameson, Geoffrey B. ; Ayoub, Alex M. ; Moorthy, Ramkumar ; Aihara, Hideki ; Harris, Reuben ; Filichev, Vyacheslav V. ; Harki, Daniel A ; Harjes, Elena. / Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2′-Deoxyzebularine Analogues. In: Biochemistry. 2019 ; Vol. 58, No. 5. pp. 391-400.
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