Related Experiment Video
Updated: Sep 9, 2025
Author Spotlight: Replicating Human Osteosarcoma Progression in Immunodeficient Mice for Cancer Study
Published on: March 22, 2024
Integrating single-cell transcriptomics, molecular docking, and dynamics simulations to characterize protein kinase
Zongye Zhang1, Zhi Sha1, Zhendong Liu2
1Zhengzhou University People's Hospital, Henan Provincial People's Hospital, China.
Background:
Osteosarcoma (OS) progression is linked to kinase allostery dysregulation, but PRKX's allosteric role remains unknown. We aimed to decode PRKX's activation mechanism and assess its clinical potential as a biomarker and therapeutic target.
Methods:
Differential expression analysis confirmed PRKX's oncogenic role. Using single-cell RNA-seq (GSE152048) with spatiotemporal trajectory analysis, we delineated PRKX-CDC37 interactions. PRKX-knockdown via siRNA suppressed proliferation, invasion, and colony formation in vitro. Based on the AlphaFold-predicted PRKX-CDC37 complex, we performed molecular docking followed by explicit-solvent 100-ns MD simulations to evaluate inhibitor binding.
Results:
Multi-omics revealed PRKX-CDC37 spatiotemporal co-expression driving early TME differentiation. Ergotamine (ΔG = -11.6 kcal/mol) competitively bound PRKX's catalytic pocket via a tripartite H-bond network centered on HIS161. MD simulations demonstrated ≥95 % occupancy H-bonds and 28.6 % SASA reduction, confirming ergotamine as the lead PRKX-CDC37 inhibitor with nanomolar-scale affinity.
Conclusion:
PRKX drives OS via a CDC37-mediated allosteric pathway, with Pocket-3 (HIS161) as a therapeutic target. Ergotamine validates PRKX-CDC37 inhibition, providing a framework for anti-OS drug design.
Insights
Protein kinase R (PRKX) drives osteosarcoma progression through a CDC37-mediated allosteric pathway. Ergotamine effectively inhibits this interaction, offering a potential therapeutic strategy for osteosarcoma treatment.
Area of Science:
- Oncology
- Molecular Biology
- Biochemistry
Background:
- Osteosarcoma (OS) progression is associated with dysregulated kinase allostery.
- The specific allosteric role of Protein Kinase R (PRKX) in OS remains uncharacterized.
- Understanding PRKX's mechanism is crucial for identifying new therapeutic targets.
Purpose of the Study:
- To elucidate the activation mechanism of PRKX in osteosarcoma.
- To investigate the potential of PRKX as a diagnostic biomarker and therapeutic target.
- To identify and validate inhibitors of the PRKX-CDC37 interaction.
Main Methods:
- Differential gene expression analysis to establish PRKX's oncogenic role.
- Single-cell RNA sequencing and spatiotemporal trajectory analysis to map PRKX-CDC37 interactions.
- In vitro PRKX knockdown studies using siRNA.
- Molecular docking and molecular dynamics (MD) simulations based on AlphaFold-predicted structures.
Main Results:
- PRKX and CDC37 exhibit spatiotemporal co-expression, driving early tumor microenvironment differentiation.
- Ergotamine demonstrated potent binding to PRKX's catalytic pocket, forming key hydrogen bonds.
- MD simulations confirmed ergotamine as a high-affinity PRKX-CDC37 inhibitor with nanomolar affinity.
Conclusions:
- PRKX promotes osteosarcoma via a CDC37-dependent allosteric pathway, targeting Pocket-3 (HIS161).
- Ergotamine effectively inhibits the PRKX-CDC37 interaction, validating it as a therapeutic target.
- This study provides a foundation for developing novel anti-osteosarcoma drugs targeting the PRKX-CDC37 axis.
