A New Class of Uracil–DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus Enzyme
Uracil–DNA glycosylases are enzymes that excise uracil bases appearing in DNA as a result of cytosine deamination or accidental dUMP incorporation from the dUTP pool. The activity of Family 1 uracil–DNA glycosylase (UNG) activity limits the efficiency of antimetabolite drugs and is essential for vir...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-11-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/26/21/6668 |
| _version_ | 1797511998013964288 |
|---|---|
| author | Inga R. Grin Grigory V. Mechetin Rustem D. Kasymov Evgeniia A. Diatlova Anna V. Yudkina Sergei N. Shchelkunov Irina P. Gileva Alexandra A. Denisova Grigoriy A. Stepanov Ghermes G. Chilov Dmitry O. Zharkov |
| author_facet | Inga R. Grin Grigory V. Mechetin Rustem D. Kasymov Evgeniia A. Diatlova Anna V. Yudkina Sergei N. Shchelkunov Irina P. Gileva Alexandra A. Denisova Grigoriy A. Stepanov Ghermes G. Chilov Dmitry O. Zharkov |
| author_sort | Inga R. Grin |
| collection | DOAJ |
| description | Uracil–DNA glycosylases are enzymes that excise uracil bases appearing in DNA as a result of cytosine deamination or accidental dUMP incorporation from the dUTP pool. The activity of Family 1 uracil–DNA glycosylase (UNG) activity limits the efficiency of antimetabolite drugs and is essential for virulence in some bacterial and viral infections. Thus, UNG is regarded as a promising target for antitumor, antiviral, antibacterial, and antiprotozoal drugs. Most UNG inhibitors presently developed are based on the uracil base linked to various substituents, yet new pharmacophores are wanted to target a wide range of UNGs. We have conducted virtual screening of a 1,027,767-ligand library and biochemically screened the best hits for the inhibitory activity against human and vaccinia virus UNG enzymes. Although even the best inhibitors had IC<sub>50</sub> ≥ 100 μM, they were highly enriched in a common fragment, tetrahydro-2,4,6-trioxopyrimidinylidene (PyO3). In silico, PyO3 preferably docked into the enzyme’s active site, and in kinetic experiments, the inhibition was better consistent with the competitive mechanism. The toxicity of two best inhibitors for human cells was independent of the presence of methotrexate, which is consistent with the hypothesis that dUMP in genomic DNA is less toxic for the cell than strand breaks arising from the massive removal of uracil. We conclude that PyO3 may be a novel pharmacophore with the potential for development into UNG-targeting agents. |
| first_indexed | 2024-03-10T05:55:46Z |
| format | Article |
| id | doaj.art-4eccb9b2add64a62a6373d3ddfe88e90 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T05:55:46Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-4eccb9b2add64a62a6373d3ddfe88e902023-11-22T21:24:44ZengMDPI AGMolecules1420-30492021-11-012621666810.3390/molecules26216668A New Class of Uracil–DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus EnzymeInga R. Grin0Grigory V. Mechetin1Rustem D. Kasymov2Evgeniia A. Diatlova3Anna V. Yudkina4Sergei N. Shchelkunov5Irina P. Gileva6Alexandra A. Denisova7Grigoriy A. Stepanov8Ghermes G. Chilov9Dmitry O. Zharkov10SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Novosibirsk 630090, RussiaSB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Novosibirsk 630090, RussiaSB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Novosibirsk 630090, RussiaSB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Novosibirsk 630090, RussiaSB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Novosibirsk 630090, RussiaDepartment of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, RussiaState Research Center of Virology and Biotechnology VECTOR, Koltsovo 630559, Novosibirsk Region, RussiaFaculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 1 Leninskie Gory, Moscow 119991, RussiaNational Research University Higher School of Economics, 20 Myasnitskaya Street, Moscow 101000, RussiaZelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Avenue, Moscow 119334, RussiaSB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Novosibirsk 630090, RussiaUracil–DNA glycosylases are enzymes that excise uracil bases appearing in DNA as a result of cytosine deamination or accidental dUMP incorporation from the dUTP pool. The activity of Family 1 uracil–DNA glycosylase (UNG) activity limits the efficiency of antimetabolite drugs and is essential for virulence in some bacterial and viral infections. Thus, UNG is regarded as a promising target for antitumor, antiviral, antibacterial, and antiprotozoal drugs. Most UNG inhibitors presently developed are based on the uracil base linked to various substituents, yet new pharmacophores are wanted to target a wide range of UNGs. We have conducted virtual screening of a 1,027,767-ligand library and biochemically screened the best hits for the inhibitory activity against human and vaccinia virus UNG enzymes. Although even the best inhibitors had IC<sub>50</sub> ≥ 100 μM, they were highly enriched in a common fragment, tetrahydro-2,4,6-trioxopyrimidinylidene (PyO3). In silico, PyO3 preferably docked into the enzyme’s active site, and in kinetic experiments, the inhibition was better consistent with the competitive mechanism. The toxicity of two best inhibitors for human cells was independent of the presence of methotrexate, which is consistent with the hypothesis that dUMP in genomic DNA is less toxic for the cell than strand breaks arising from the massive removal of uracil. We conclude that PyO3 may be a novel pharmacophore with the potential for development into UNG-targeting agents.https://www.mdpi.com/1420-3049/26/21/6668DNA repairuracil–DNA glycosylaseinhibitorsvirtual screeningpyrimidines |
| spellingShingle | Inga R. Grin Grigory V. Mechetin Rustem D. Kasymov Evgeniia A. Diatlova Anna V. Yudkina Sergei N. Shchelkunov Irina P. Gileva Alexandra A. Denisova Grigoriy A. Stepanov Ghermes G. Chilov Dmitry O. Zharkov A New Class of Uracil–DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus Enzyme Molecules DNA repair uracil–DNA glycosylase inhibitors virtual screening pyrimidines |
| title | A New Class of Uracil–DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus Enzyme |
| title_full | A New Class of Uracil–DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus Enzyme |
| title_fullStr | A New Class of Uracil–DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus Enzyme |
| title_full_unstemmed | A New Class of Uracil–DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus Enzyme |
| title_short | A New Class of Uracil–DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus Enzyme |
| title_sort | new class of uracil dna glycosylase inhibitors active against human and vaccinia virus enzyme |
| topic | DNA repair uracil–DNA glycosylase inhibitors virtual screening pyrimidines |
| url | https://www.mdpi.com/1420-3049/26/21/6668 |
| work_keys_str_mv | AT ingargrin anewclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT grigoryvmechetin anewclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT rustemdkasymov anewclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT evgeniiaadiatlova anewclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT annavyudkina anewclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT sergeinshchelkunov anewclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT irinapgileva anewclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT alexandraadenisova anewclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT grigoriyastepanov anewclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT ghermesgchilov anewclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT dmitryozharkov anewclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT ingargrin newclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT grigoryvmechetin newclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT rustemdkasymov newclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT evgeniiaadiatlova newclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT annavyudkina newclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT sergeinshchelkunov newclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT irinapgileva newclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT alexandraadenisova newclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT grigoriyastepanov newclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT ghermesgchilov newclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme AT dmitryozharkov newclassofuracildnaglycosylaseinhibitorsactiveagainsthumanandvacciniavirusenzyme |