Investigating the inhibitory potential of natural bioactive compounds against cyclin-dependent kinase 13: virtual high throughput screening and MD simulation studies to target CDK signaling.

Abstract

Cyclin-dependent kinase 13 (CDK13) belongs to the cyclin-dependent kinase (CDK) family that is actively involved in transcription regulation and RNA splicing. CDK13 binds with its partner, cyclin K, to regulate several biological processes. CDK13 and cyclin K complex phosphorylates RNA pol II carboxyl-terminal domain (CTD) at several serine residues, creating transcription elongation. The upregulation of the kinase contributes to tumor growth and cell proliferation, and is highly associated with various cancers, including skin, stomach, and ovarian. Thus, it can be considered an efficient therapeutic target for the development of drugs against cancer. In this work, a virtual high throughput screening (vHTS) of the ZINC library was carried out to elucidate the initial potent compounds. Further, filters were applied to identify the hit compounds among the ∼90,000 compound library. Based on the docking scores and binding affinity, the top 100 hits were elucidated, and they were further narrowed down to 50 compounds based on ADMET and Lipinski's RO5 filter. Finally, 10 compounds were chosen that showed appreciable biological activity. Among them, ZINC02136558 was selected as a potent lead compound that showed strong interaction with the amino acid residues of active and binding sites of CDK13. Furthermore, the all-atom molecular dynamic simulation was performed at 200 ns to explore the dynamic evolution of the system. Finally, the results showed that the ZINC02136558 may be considered as a potential lead molecule to inhibit CDK13 and implicated in therapeutic management of cancer and associated diseases.