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Updated: Apr 25, 2026

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
Published on: June 27, 2020
Transcriptomics-driven identification of CDK1 as a central oncogenic driver in TNBC: an in silico structural modeling
Uma Chaudhary1, Sidharth Kumar Nanda Kumar2, Magesh Ramaswamy2
1Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
Introduction:
Triple-negative breast cancer (TNBC) is an aggressive subtype that lacks ER, PR, and HER2 receptors, which limits the availability of targeted therapies. In this study, we analyzed CDK1 as a potential molecular target and evaluated natural compounds that might inhibit its activity.
Methods:
Transcriptomic comparison revealed 85 commonly upregulated mRNAs in TNBC, and functional enrichment combined with PPI network analysis indicated CDK1 as a major hub gene. To search for potential inhibitors, we screened an anticancer-focused phytochemical library from the SuperNatural 3.0 database using molecular docking followed by ADMET assessment.
Results:
Among the screened molecules, CID17584963 showed the strongest binding energy (-8.09 kcal/mol) and displayed pharmacokinetic properties comparable to or better than those of paclitaxel. Long-timescale (500 ns) molecular dynamics simulations further supported the stability of the CDK1-CID17584963 complex, with root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration, solvent-accessible surface area (SASA), hydrogen-bond profiles, and principal component analysis (PCA) all indicating consistent interactions throughout the trajectory.
Discussion:
Taken together, these findings indicate that CID17584963 interacts with CDK1 more stably than the reference drug and may serve as a promising natural compound for further studies in TNBC therapy.
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