Selective CDK9 Inhibition by Natural Compound Toyocamycin in Cancer Cells
Aberrant transcription in cancer cells involves the silencing of tumor suppressor genes (TSGs) and activation of oncogenes. Transcriptomic changes are associated with epigenomic alterations such as DNA-hypermethylation, histone deacetylation, and chromatin condensation in promoter regions of silence...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-07-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/14/14/3340 |
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| author | Somnath Pandey Rahinatou Djibo Anaïs Darracq Gennaro Calendo Hanghang Zhang Ryan A. Henry Andrew J. Andrews Stephen B. Baylin Jozef Madzo Rafael Najmanovich Jean-Pierre J. Issa Noël J.-M. Raynal |
| author_facet | Somnath Pandey Rahinatou Djibo Anaïs Darracq Gennaro Calendo Hanghang Zhang Ryan A. Henry Andrew J. Andrews Stephen B. Baylin Jozef Madzo Rafael Najmanovich Jean-Pierre J. Issa Noël J.-M. Raynal |
| author_sort | Somnath Pandey |
| collection | DOAJ |
| description | Aberrant transcription in cancer cells involves the silencing of tumor suppressor genes (TSGs) and activation of oncogenes. Transcriptomic changes are associated with epigenomic alterations such as DNA-hypermethylation, histone deacetylation, and chromatin condensation in promoter regions of silenced TSGs. To discover novel drugs that trigger TSG reactivation in cancer cells, we used a GFP-reporter system whose expression is silenced by promoter DNA hypermethylation and histone deacetylation. After screening a natural product drug library, we identified that toyocamycin, an adenosine-analog, induces potent GFP reactivation and loss of clonogenicity in human colon cancer cells. Connectivity-mapping analysis revealed that toyocamycin produces a pharmacological signature mimicking cyclin-dependent kinase (CDK) inhibitors. RNA-sequencing revealed that the toyocamycin transcriptomic signature resembles that of a specific CDK9 inhibitor (HH1). Specific inhibition of RNA Pol II phosphorylation level and kinase assays confirmed that toyocamycin specifically inhibits CDK9 (IC<sub>50</sub> = 79 nM) with a greater efficacy than other CDKs (IC<sub>50</sub> values between 0.67 and 15 µM). Molecular docking showed that toyocamycin efficiently binds the CDK9 catalytic site in a conformation that differs from other CDKs, explained by the binding contribution of specific amino acids within the catalytic pocket and protein backbone. Altogether, we demonstrated that toyocamycin exhibits specific CDK9 inhibition in cancer cells, highlighting its potential for cancer chemotherapy. |
| first_indexed | 2024-03-09T10:20:59Z |
| format | Article |
| id | doaj.art-283af2a4bd9a464da79dad1390a6ea5c |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-09T10:20:59Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-283af2a4bd9a464da79dad1390a6ea5c2023-12-01T21:59:09ZengMDPI AGCancers2072-66942022-07-011414334010.3390/cancers14143340Selective CDK9 Inhibition by Natural Compound Toyocamycin in Cancer CellsSomnath Pandey0Rahinatou Djibo1Anaïs Darracq2Gennaro Calendo3Hanghang Zhang4Ryan A. Henry5Andrew J. Andrews6Stephen B. Baylin7Jozef Madzo8Rafael Najmanovich9Jean-Pierre J. Issa10Noël J.-M. Raynal11Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USADépartement de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC H3T 1J4, CanadaDépartement de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC H3T 1J4, CanadaCoriell Institute for Medical Research, Camden, NJ 08103, USAFels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USADepartment of Chemistry and Biochemistry, Wilkes University, Wilkes-Barre, PA 18766, USADepartment of Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA 19111, USAThe Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USAFels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USADépartement de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC H3T 1J4, CanadaFels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USADépartement de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC H3T 1J4, CanadaAberrant transcription in cancer cells involves the silencing of tumor suppressor genes (TSGs) and activation of oncogenes. Transcriptomic changes are associated with epigenomic alterations such as DNA-hypermethylation, histone deacetylation, and chromatin condensation in promoter regions of silenced TSGs. To discover novel drugs that trigger TSG reactivation in cancer cells, we used a GFP-reporter system whose expression is silenced by promoter DNA hypermethylation and histone deacetylation. After screening a natural product drug library, we identified that toyocamycin, an adenosine-analog, induces potent GFP reactivation and loss of clonogenicity in human colon cancer cells. Connectivity-mapping analysis revealed that toyocamycin produces a pharmacological signature mimicking cyclin-dependent kinase (CDK) inhibitors. RNA-sequencing revealed that the toyocamycin transcriptomic signature resembles that of a specific CDK9 inhibitor (HH1). Specific inhibition of RNA Pol II phosphorylation level and kinase assays confirmed that toyocamycin specifically inhibits CDK9 (IC<sub>50</sub> = 79 nM) with a greater efficacy than other CDKs (IC<sub>50</sub> values between 0.67 and 15 µM). Molecular docking showed that toyocamycin efficiently binds the CDK9 catalytic site in a conformation that differs from other CDKs, explained by the binding contribution of specific amino acids within the catalytic pocket and protein backbone. Altogether, we demonstrated that toyocamycin exhibits specific CDK9 inhibition in cancer cells, highlighting its potential for cancer chemotherapy.https://www.mdpi.com/2072-6694/14/14/3340CDKsCDK9 inhibitortoyocamycindrug screeningepigeneticscancer |
| spellingShingle | Somnath Pandey Rahinatou Djibo Anaïs Darracq Gennaro Calendo Hanghang Zhang Ryan A. Henry Andrew J. Andrews Stephen B. Baylin Jozef Madzo Rafael Najmanovich Jean-Pierre J. Issa Noël J.-M. Raynal Selective CDK9 Inhibition by Natural Compound Toyocamycin in Cancer Cells Cancers CDKs CDK9 inhibitor toyocamycin drug screening epigenetics cancer |
| title | Selective CDK9 Inhibition by Natural Compound Toyocamycin in Cancer Cells |
| title_full | Selective CDK9 Inhibition by Natural Compound Toyocamycin in Cancer Cells |
| title_fullStr | Selective CDK9 Inhibition by Natural Compound Toyocamycin in Cancer Cells |
| title_full_unstemmed | Selective CDK9 Inhibition by Natural Compound Toyocamycin in Cancer Cells |
| title_short | Selective CDK9 Inhibition by Natural Compound Toyocamycin in Cancer Cells |
| title_sort | selective cdk9 inhibition by natural compound toyocamycin in cancer cells |
| topic | CDKs CDK9 inhibitor toyocamycin drug screening epigenetics cancer |
| url | https://www.mdpi.com/2072-6694/14/14/3340 |
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