2. Academic Validation
  3. Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans

Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans

  • mBio. 2025 Dec 10;16(12):e0289825. doi: 10.1128/mbio.02898-25.
Pooja Sethiya 1 2,  Desmarini Desmarini 1 2,  Bethany Grace Bowring 1 2,  Kyle Cesar 3,  Michael J Boucher 3,  Angela L Wei 3,  Hiten D Madhani 3,  Ben Crossett 4,  Angela Connelly 4,  Catriona L Halliday 5,  Sharon C-A Chen 2 5 6,  Joey Lai 7,  Koon Ho Wong 8,  Julianne Teresa Djordjevic 1 2 6
Affiliations

Affiliations

  • 1 Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.
  • 2 Faculty of Medicine and Health, Sydney Institute for Infectious Diseases, University of Sydney, Camperdown, New South Wales, Australia.
  • 3 Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA.
  • 4 Sydney Mass Spectrometry, University of Sydney, Camperdown, New South Wales, Australia.
  • 5 Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia.
  • 6 Westmead Hospital, Westmead, New South Wales, Australia.
  • 7 Scientific Platforms, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.
  • 8 Faculty of Health Sciences, University of Macau, Macau SAR, China.
PMID: 41171060 DOI: 10.1128/mbio.02898-25
Abstract

Cyclin-dependent kinase (CDK)7 regulates the cell cycle and transcription in higher eukaryotes, but its function and the Antifungal potential of CDK7 inhibitors remain unexplored in Fungal pathogens. CDK7 inhibitors were identified to probe CDK7 function in the priority Fungal pathogen, Cryptococcus neoformans (Cn). The CDK7 ortholog in Cn was tagged with mNeonGreen and shown to form a nuclear-localized, CDK-activating kinase (CAK) complex with cyclin H and assembly factor Mat1. The pulled-down CAK complex was demonstrated to be active and was used to identify several human CDK7 inhibitors that also inhibit CnCDK7 enzyme activity. In addition to inhibiting CnCDK7 enzyme activity, the compound mevociclib (SY-1365) most significantly inhibited Fungal growth and was deployed to probe CnCDK7 function using multi-omics analysis, flow cytometry, and Western blotting, with roles in transcription via RNA polymerase II phosphorylation, mRNA splicing, and progression through G2/M of the cell cycle identified. Inhibition of CDK7 also suppressed MAP kinase (Hog1) signaling. Notably, compound SY-1365 and related inhibitors synergized with licensed, membrane-targeting antifungals at low micromolar concentrations against both C. neoformans and Cryptococcus gattii. Our findings establish SY-1365 as a powerful chemical probe to define CDK7 function in Cn and suggest that its role more closely resembles that in human cells than in model fungi. Furthermore, given that CDK7 inhibitors are used in oncology, our findings identify CDK7 inhibitors as promising Antifungal candidates for combination therapy with licensed antifungals, with the potential to overcome current challenges associated with toxicity and Antifungal resistance.

Importance: Cn, a basidiomycete causing meningoencephalitis with 40%-60% mortality, was recently assigned as a "critical" priority pathogen by the World Health Organization. Cn commonly affects AIDS patients, organ transplant recipients, and individuals with hematological malignancies, yet current treatments are limited by toxicity or resistance due to prolonged therapy. Given that CDK7 inhibitors kill leukemia cells, and Cn proliferation in host tissues mimics tumor-like growth, we investigated whether their utility as Anticancer agents extends to Antifungal activity and elucidation of CDK7 function in Cn. Use of SY-1365, which was both Antifungal and CnCDK7 inhibitory, identified roles for CnCDK7 in all stages of transcription, mRNA splicing, and cell cycle regulation. The Antifungal activity of SY-1365 was also markedly enhanced in combination with membrane-targeting antifungals. Together, our findings highlight CDK7 inhibitors as valuable tools to study CDK7 function in Cn and as potentially promising antifungals in combination with licensed antifungals.

Keywords

CAK complex; CDK7; CDK7-IN-3; Cryptococcus neoformans; Hog1; MAPK; RNAPII; SY-1365; SY-5609; cell cycle; mevociclib; samuraciclib; splicing; transcription.

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