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Updated: Jun 27, 2026
Identification of Kinase-substrate Pairs Using High Throughput Screening
Published on: August 29, 2015
Identification and Validation of New DNA-PKcs Inhibitors through High-Throughput Virtual Screening and Experimental
Liujiang Dai1,2, Pengfei Yu3, Hongjie Fan3
1Department of Physiology, Guangxi University of Chinese Medicine, Nanning 530200, China.
Abstract:
DNA-PKcs is a crucial protein target involved in DNA repair and response pathways, with its abnormal activity closely associated with the occurrence and progression of various cancers. In this study, we employed a deep learning-based screening and molecular dynamics (MD) simulation-based pipeline, identifying eight candidates for DNA-PKcs targets. Subsequent experiments revealed the effective inhibition of DNA-PKcs-mediated cell proliferation by three small molecules (5025-0002, M769-1095, and V008-1080). These molecules exhibited anticancer activity with IC50 (inhibitory concentration at 50%) values of 152.6 μM, 30.71 μM, and 74.84 μM, respectively. Notably, V008-1080 enhanced homology-directed repair (HDR) mediated by CRISPR/Cas9 while inhibiting non-homologous end joining (NHEJ) efficiency. Further investigations into the structure-activity relationships unveiled the binding sites and critical interactions between these small molecules and DNA-PKcs. This is the first application of DeepBindGCN_RG in a real drug screening task, and the successful discovery of a novel DNA-PKcs inhibitor demonstrates its efficiency as a core component in the screening pipeline. Moreover, this study provides important insights for exploring novel anticancer therapeutics and advancing the development of gene editing techniques by targeting DNA-PKcs.
Insights
Researchers identified novel small molecules targeting DNA-PKcs, a protein linked to cancer. These inhibitors show anticancer activity and offer potential for new cancer therapies and gene editing advancements.
Area of Science:
- Biochemistry
- Molecular Biology
- Pharmacology
Background:
- DNA-Protein Kinase catalytic subunit (DNA-PKcs) is vital in DNA repair and cellular responses.
- Aberrant DNA-PKcs activity correlates with cancer occurrence and progression, making it a key therapeutic target.
Purpose of the Study:
- To discover novel small molecules that inhibit DNA-PKcs activity.
- To explore the potential of these inhibitors as anticancer therapeutics.
- To investigate their impact on DNA repair pathways and gene editing techniques.
Main Methods:
- Utilized a deep learning-based screening pipeline combined with molecular dynamics (MD) simulations to identify potential DNA-PKcs inhibitors.
- Conducted experimental validation of candidate molecules, assessing their efficacy in inhibiting DNA-PKcs-mediated cell proliferation.
- Performed structure-activity relationship (SAR) studies to understand molecular interactions and binding sites.
Main Results:
- Identified eight candidate small molecules, with three (5025-0002, M769-1095, V008-1080) demonstrating effective inhibition of DNA-PKcs.
- Determined IC50 values for the active compounds, indicating varying potencies (152.6 μM, 30.71 μM, 74.84 μM).
- Observed that V008-1080 selectively enhanced CRISPR/Cas9-mediated homology-directed repair (HDR) while suppressing non-homologous end joining (NHEJ).
Conclusions:
- The study successfully identified novel small molecule inhibitors of DNA-PKcs using an integrated deep learning and MD simulation approach.
- The discovered compounds, particularly V008-1080, show promise as anticancer agents and tools for modulating DNA repair pathways.
- This research validates the efficacy of the DeepBindGCN_RG pipeline for drug discovery and provides a foundation for developing targeted cancer therapies and advancing gene editing technologies.
