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Updated: Jan 20, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Discovery of New Inhibitors of Transforming Growth Factor-Beta Type 1 Receptor by Utilizing Docking and
1College of Pharmacy, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China.
Abstract:
The transforming growth factor-beta (TGF-β) plays an important role in pathological fibrosis and cancer transformation. Therefore, the inhibition of the TGF-β signaling pathway has therapeutic potential in the treatment of cancer. In this study, the binding modes between 47 molecules with a pyrrolotriazine-like backbone structure and transforming growth factor-beta type 1 receptor (TβR1) were simulated by molecular docking using Discovery Studio software, and their structure-activity relationships were analyzed. On the basis of the analysis of the binding modes of ligands in the active site and the structure-activity relationships, 29,254 new compounds were designed for virtual screening. According to the aforementioned analyses and Lipinski's rule of five, five new compounds (CQMU1901-1905) with potential activity were screened through molecular docking. Among them, CQMU1905 is an attractive molecule composed of 5-fluorouracil (5-FU), 6-mercaptopurine (6-MP), and 5-azacytosine. Interestingly, 5-FU, 6-MP, and 5-azacytidine are often used as anti-metabolic agents in cancer treatment. Compared with existing compounds, CQMU1901-1905 can interact with target proteins more effectively and have good potential for modification, making them worthy of further study.
Insights
Researchers identified novel pyrrolotriazine compounds that effectively inhibit the transforming growth factor-beta (TGF-β) signaling pathway, offering new therapeutic strategies for cancer treatment.
Area of Science:
- Medicinal Chemistry
- Molecular Biology
- Computational Drug Design
Background:
- Transforming growth factor-beta (TGF-β) signaling is implicated in pathological fibrosis and cancer progression.
- Inhibiting the TGF-β pathway presents a promising therapeutic strategy for various cancers.
Purpose of the Study:
- To design and screen novel pyrrolotriazine-based compounds targeting the TGF-β type 1 receptor (TβR1).
- To analyze structure-activity relationships and identify potent inhibitors for cancer therapy.
Main Methods:
- Molecular docking simulations were employed to analyze binding modes of 47 pyrrolotriazine derivatives with TβR1.
- Structure-activity relationships were evaluated, leading to the design of 29,254 new virtual compounds.
- Lipinski's rule of five and molecular docking guided the selection of five potential drug candidates (CQMU1901-1905).
Main Results:
- The study identified five novel compounds (CQMU1901-1905) with potential TβR1 inhibitory activity.
- CQMU1905, a combination of 5-fluorouracil, 6-mercaptopurine, and 5-azacytosine, showed particular promise.
- The identified compounds demonstrated superior interaction with target proteins compared to existing agents.
Conclusions:
- The novel pyrrolotriazine compounds (CQMU1901-1905) show significant potential for inhibiting the TGF-β pathway in cancer.
- CQMU1905 represents an attractive candidate due to its composition and potential efficacy.
- These compounds warrant further investigation for their therapeutic applications in oncology.
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