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Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A
The APOBEC3 (APOBEC3A-H) enzyme family as a part of the human innate immune system deaminates cytosine to uracil in single-stranded DNA (ssDNA) and thereby prevents the spread of pathogenic genetic information. However, APOBEC3-induced mutagenesis promotes viral and cancer evolution, thus enabling t...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Royal Society of Chemistry
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10282898/ https://www.ncbi.nlm.nih.gov/pubmed/37282621 http://dx.doi.org/10.1039/d3ob00392b |
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author | Kurup, Harikrishnan M. Kvach, Maksim V. Harjes, Stefan Jameson, Geoffrey B. Harjes, Elena Filichev, Vyacheslav V. |
author_facet | Kurup, Harikrishnan M. Kvach, Maksim V. Harjes, Stefan Jameson, Geoffrey B. Harjes, Elena Filichev, Vyacheslav V. |
author_sort | Kurup, Harikrishnan M. |
collection | PubMed |
description | The APOBEC3 (APOBEC3A-H) enzyme family as a part of the human innate immune system deaminates cytosine to uracil in single-stranded DNA (ssDNA) and thereby prevents the spread of pathogenic genetic information. However, APOBEC3-induced mutagenesis promotes viral and cancer evolution, thus enabling the progression of diseases and development of drug resistance. Therefore, APOBEC3 inhibition offers a possibility to complement existing antiviral and anticancer therapies and prevent the emergence of drug resistance, thus making such therapies effective for longer periods of time. Here, we synthesised nucleosides containing seven-membered nucleobases based on azepinone and compared their inhibitory potential against human cytidine deaminase (hCDA) and APOBEC3A with previously described 2′-deoxyzebularine (dZ) and 5-fluoro-2′-deoxyzebularine (FdZ). The nanomolar inhibitor of wild-type APOBEC3A was obtained by the incorporation of 1,3,4,7-tetrahydro-2H-1,3-diazepin-2-one in the TTC loop of a DNA hairpin instead of the target 2′-deoxycytidine providing a K(i) of 290 ± 40 nM, which is only slightly weaker than the K(i) of the FdZ-containing inhibitor (117 ± 15 nM). A less potent but notably different inhibition of human cytidine deaminase (CDA) and engineered C-terminal domain of APOBEC3B was observed for 2′-deoxyribosides of the S and R isomers of hexahydro-5-hydroxy-azepin-2-one: the S-isomer was more active than the R-isomer. The S-isomer shows resemblance in the position of the OH-group observed recently for the hydrated dZ and FdZ in the crystal structures with APOBEC3G and APOBEC3A, respectively. This shows that 7-membered ring analogues of pyrimidine nucleosides can serve as a platform for further development of modified ssDNAs as powerful A3 inhibitors. |
format | Online Article Text |
id | pubmed-10282898 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | The Royal Society of Chemistry |
record_format | MEDLINE/PubMed |
spelling | pubmed-102828982023-06-22 Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A Kurup, Harikrishnan M. Kvach, Maksim V. Harjes, Stefan Jameson, Geoffrey B. Harjes, Elena Filichev, Vyacheslav V. Org Biomol Chem Chemistry The APOBEC3 (APOBEC3A-H) enzyme family as a part of the human innate immune system deaminates cytosine to uracil in single-stranded DNA (ssDNA) and thereby prevents the spread of pathogenic genetic information. However, APOBEC3-induced mutagenesis promotes viral and cancer evolution, thus enabling the progression of diseases and development of drug resistance. Therefore, APOBEC3 inhibition offers a possibility to complement existing antiviral and anticancer therapies and prevent the emergence of drug resistance, thus making such therapies effective for longer periods of time. Here, we synthesised nucleosides containing seven-membered nucleobases based on azepinone and compared their inhibitory potential against human cytidine deaminase (hCDA) and APOBEC3A with previously described 2′-deoxyzebularine (dZ) and 5-fluoro-2′-deoxyzebularine (FdZ). The nanomolar inhibitor of wild-type APOBEC3A was obtained by the incorporation of 1,3,4,7-tetrahydro-2H-1,3-diazepin-2-one in the TTC loop of a DNA hairpin instead of the target 2′-deoxycytidine providing a K(i) of 290 ± 40 nM, which is only slightly weaker than the K(i) of the FdZ-containing inhibitor (117 ± 15 nM). A less potent but notably different inhibition of human cytidine deaminase (CDA) and engineered C-terminal domain of APOBEC3B was observed for 2′-deoxyribosides of the S and R isomers of hexahydro-5-hydroxy-azepin-2-one: the S-isomer was more active than the R-isomer. The S-isomer shows resemblance in the position of the OH-group observed recently for the hydrated dZ and FdZ in the crystal structures with APOBEC3G and APOBEC3A, respectively. This shows that 7-membered ring analogues of pyrimidine nucleosides can serve as a platform for further development of modified ssDNAs as powerful A3 inhibitors. The Royal Society of Chemistry 2023-06-07 /pmc/articles/PMC10282898/ /pubmed/37282621 http://dx.doi.org/10.1039/d3ob00392b Text en This journal is © The Royal Society of Chemistry https://creativecommons.org/licenses/by-nc/3.0/ |
spellingShingle | Chemistry Kurup, Harikrishnan M. Kvach, Maksim V. Harjes, Stefan Jameson, Geoffrey B. Harjes, Elena Filichev, Vyacheslav V. Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A |
title | Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A |
title_full | Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A |
title_fullStr | Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A |
title_full_unstemmed | Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A |
title_short | Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A |
title_sort | seven-membered ring nucleobases as inhibitors of human cytidine deaminase and apobec3a |
topic | Chemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10282898/ https://www.ncbi.nlm.nih.gov/pubmed/37282621 http://dx.doi.org/10.1039/d3ob00392b |
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