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Target screening and optimization of candidate compounds for breast cancer treatment using bioinformatics and computational chemistry approaches.

作者信息

Xu Jian, Li Xue, Jia Yiduo

机构信息

Shaoxing People's Hospital, Shaoxing, China.

School of Medicine and Pharmacy, Wuhan University of Bioengineering, Wuhan, China.

出版信息

Front Pharmacol. 2025 May 9;16:1467504. doi: 10.3389/fphar.2025.1467504. eCollection 2025.


DOI:10.3389/fphar.2025.1467504
PMID:40417221
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12098522/
Abstract

OBJECTIVES: This study aimed to identify critical therapeutic targets and design potent antitumor compounds for breast cancer treatment through an integrated bioinformatics and computational chemistry approach. METHODS: We conducted initial screening and target intersection analysis to identify potential protein targets, highlighting the adenosine A1 receptor as a key candidate. Molecular docking and molecular dynamics (MD) simulations were performed to evaluate the binding stability between selected compounds and the human adenosine A1 receptor-Gi2 protein complex (PDB ID: 7LD3). A pharmacophore model was constructed based on binding information to guide the virtual screening of additional compounds with activity. Furthermore, we designed and synthesized a novel molecule based on this model, followed by biological evaluation using MCF-7 breast cancer cells. RESULTS: Compound 5 exhibited stable binding to the adenosine A1 receptor, as confirmed by docking and MD simulations. Pharmacophore-based screening identified compounds 6-9 with strong binding affinities. These findings guided Molecule 10, which was rationally designed and synthesized, showing potent antitumor activity against MCF-7 cells with an IC50 value of 0.032 µM, significantly outperforming the positive control 5-FU (IC50 = 0.45 µM). CONCLUSION: This study advances the understanding of molecular interactions in breast cancer therapy and demonstrates the potential of Molecule 10 as a highly effective therapeutic candidate. Integrating reverse drug screening, molecular modelling, and validation provides a robust platform for future drug discovery in breast cancer treatment.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/e1a64d1112c9/fphar-16-1467504-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/2dfa3c90cccf/FPHAR_fphar-2025-1467504_wc_sch1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/969e5e6bf7fe/fphar-16-1467504-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/8abebecc42f1/fphar-16-1467504-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/07a98c319c31/fphar-16-1467504-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/42ad561a7e01/fphar-16-1467504-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/e1a64d1112c9/fphar-16-1467504-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/2dfa3c90cccf/FPHAR_fphar-2025-1467504_wc_sch1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/969e5e6bf7fe/fphar-16-1467504-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/8abebecc42f1/fphar-16-1467504-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/07a98c319c31/fphar-16-1467504-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/42ad561a7e01/fphar-16-1467504-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e16d/12098522/e1a64d1112c9/fphar-16-1467504-g005.jpg

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本文引用的文献

[1]
Alpha-mangostin and nab-paclitaxel in breast cancer cell models: improved antitumor efficacy through combination therapy.

Cell Mol Biol (Noisy-le-grand). 2025-2-2

[2]
The immunotoxin targeting PRLR increases tamoxifen sensitivity and enhances the efficacy of chemotherapy in breast cancer.

J Exp Clin Cancer Res. 2024-6-20

[3]
Thwarting resistance: MgrA inhibition with methylophiopogonanone a unveils a new battlefront against S. aureus.

NPJ Biofilms Microbiomes. 2024-2-27

[4]
Nanoparticle-Based Antioxidants in Stress Signaling and Programmed Cell Death in Breast Cancer Treatment.

Molecules. 2023-7-10

[5]
Omics-Based Investigations of Breast Cancer.

Molecules. 2023-6-14

[6]
A review from biological mapping to computation-based subcellular localization.

Mol Ther Nucleic Acids. 2023-4-20

[7]
In silico study of HASDI (high-affinity selective DNA intercalator) as a new agent capable of highly selective recognition of the DNA sequence.

Sci Rep. 2023-4-3

[8]
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS.

BMC Bioinformatics. 2023-3-22

[9]
The inhibitory effect and mechanism of Resina Draconis on the proliferation of MCF-7 breast cancer cells: a network pharmacology-based analysis.

Sci Rep. 2023-3-7

[10]
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.

Proc Natl Acad Sci U S A. 2023-1-10

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