Discovery of 3-Amino-1<i>H</i>-pyrazole-Based Kinase Inhibitors to Illuminate the Understudied PCTAIRE Family
The PCTAIRE subfamily belongs to the CDK (cyclin-dependent kinase) family and represents an understudied class of kinases of the dark kinome. They exhibit a highly conserved binding pocket and are activated by cyclin Y binding. CDK16 is targeted to the plasma membrane after binding to <i>N<...
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MDPI AG
2022-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/23/14834 |
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| author | Jennifer Alisa Amrhein Lena Marie Berger Amelie Tjaden Andreas Krämer Lewis Elson Tuomas Tolvanen Daniel Martinez-Molina Astrid Kaiser Manfred Schubert-Zsilavecz Susanne Müller Stefan Knapp Thomas Hanke |
| author_facet | Jennifer Alisa Amrhein Lena Marie Berger Amelie Tjaden Andreas Krämer Lewis Elson Tuomas Tolvanen Daniel Martinez-Molina Astrid Kaiser Manfred Schubert-Zsilavecz Susanne Müller Stefan Knapp Thomas Hanke |
| author_sort | Jennifer Alisa Amrhein |
| collection | DOAJ |
| description | The PCTAIRE subfamily belongs to the CDK (cyclin-dependent kinase) family and represents an understudied class of kinases of the dark kinome. They exhibit a highly conserved binding pocket and are activated by cyclin Y binding. CDK16 is targeted to the plasma membrane after binding to <i>N</i>-myristoylated cyclin Y and is highly expressed in post-mitotic tissues, such as the brain and testis. Dysregulation is associated with several diseases, including breast, prostate, and cervical cancer. Here, we used the <i>N</i>-(1<i>H</i>-pyrazol-3-yl)pyrimidin-4-amine moiety from the promiscuous inhibitor <b>1</b> to target CDK16, by varying different residues. Further optimization steps led to <b>43d</b>, which exhibited high cellular potency for CDK16 (EC<sub>50</sub> = 33 nM) and the other members of the PCTAIRE and PFTAIRE family with 20–120 nM and 50–180 nM, respectively. A DSF screen against a representative panel of approximately 100 kinases exhibited a selective inhibition over the other kinases. In a viability assessment, <b>43d</b> decreased the cell count in a dose-dependent manner. A FUCCI cell cycle assay revealed a G2/M phase cell cycle arrest at all tested concentrations for <b>43d</b>, caused by inhibition of CDK16. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T17:46:19Z |
| publishDate | 2022-11-01 |
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| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-3d8f7e84ed404e629202c35e560411a42023-11-24T11:08:44ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-11-0123231483410.3390/ijms232314834Discovery of 3-Amino-1<i>H</i>-pyrazole-Based Kinase Inhibitors to Illuminate the Understudied PCTAIRE FamilyJennifer Alisa Amrhein0Lena Marie Berger1Amelie Tjaden2Andreas Krämer3Lewis Elson4Tuomas Tolvanen5Daniel Martinez-Molina6Astrid Kaiser7Manfred Schubert-Zsilavecz8Susanne Müller9Stefan Knapp10Thomas Hanke11Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, GermanyInstitute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, GermanyInstitute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, GermanyInstitute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, GermanyInstitute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, GermanyDivision of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institute, Solnavägen 1, 17177 Solna, SwedenPelago Bioscience AB, Scheeles Väg 1, 17165 Solna, SwedenInstitute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, GermanyInstitute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, GermanyInstitute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, GermanyInstitute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, GermanyInstitute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, GermanyThe PCTAIRE subfamily belongs to the CDK (cyclin-dependent kinase) family and represents an understudied class of kinases of the dark kinome. They exhibit a highly conserved binding pocket and are activated by cyclin Y binding. CDK16 is targeted to the plasma membrane after binding to <i>N</i>-myristoylated cyclin Y and is highly expressed in post-mitotic tissues, such as the brain and testis. Dysregulation is associated with several diseases, including breast, prostate, and cervical cancer. Here, we used the <i>N</i>-(1<i>H</i>-pyrazol-3-yl)pyrimidin-4-amine moiety from the promiscuous inhibitor <b>1</b> to target CDK16, by varying different residues. Further optimization steps led to <b>43d</b>, which exhibited high cellular potency for CDK16 (EC<sub>50</sub> = 33 nM) and the other members of the PCTAIRE and PFTAIRE family with 20–120 nM and 50–180 nM, respectively. A DSF screen against a representative panel of approximately 100 kinases exhibited a selective inhibition over the other kinases. In a viability assessment, <b>43d</b> decreased the cell count in a dose-dependent manner. A FUCCI cell cycle assay revealed a G2/M phase cell cycle arrest at all tested concentrations for <b>43d</b>, caused by inhibition of CDK16.https://www.mdpi.com/1422-0067/23/23/14834CDK16cell cycleFUCCIkinasekinase inhibitorNanoBRET |
| spellingShingle | Jennifer Alisa Amrhein Lena Marie Berger Amelie Tjaden Andreas Krämer Lewis Elson Tuomas Tolvanen Daniel Martinez-Molina Astrid Kaiser Manfred Schubert-Zsilavecz Susanne Müller Stefan Knapp Thomas Hanke Discovery of 3-Amino-1<i>H</i>-pyrazole-Based Kinase Inhibitors to Illuminate the Understudied PCTAIRE Family International Journal of Molecular Sciences CDK16 cell cycle FUCCI kinase kinase inhibitor NanoBRET |
| title | Discovery of 3-Amino-1<i>H</i>-pyrazole-Based Kinase Inhibitors to Illuminate the Understudied PCTAIRE Family |
| title_full | Discovery of 3-Amino-1<i>H</i>-pyrazole-Based Kinase Inhibitors to Illuminate the Understudied PCTAIRE Family |
| title_fullStr | Discovery of 3-Amino-1<i>H</i>-pyrazole-Based Kinase Inhibitors to Illuminate the Understudied PCTAIRE Family |
| title_full_unstemmed | Discovery of 3-Amino-1<i>H</i>-pyrazole-Based Kinase Inhibitors to Illuminate the Understudied PCTAIRE Family |
| title_short | Discovery of 3-Amino-1<i>H</i>-pyrazole-Based Kinase Inhibitors to Illuminate the Understudied PCTAIRE Family |
| title_sort | discovery of 3 amino 1 i h i pyrazole based kinase inhibitors to illuminate the understudied pctaire family |
| topic | CDK16 cell cycle FUCCI kinase kinase inhibitor NanoBRET |
| url | https://www.mdpi.com/1422-0067/23/23/14834 |
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