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Targeting necroptosis in MCF-7 breast cancer cells: In Silico insights into 8,12-dimethoxysanguinarine from Eomecon Chionantha through molecular docking, dynamics, DFT, and MEP studies.

期刊 PloS one
发表日期 2025
DOI -
PMID 39775383
原始摘要

Breast cancer remains a significant challenge in oncology, highlighting the need for alternative therapeutic strategies that target necroptosis to overcome resistance to conventional therapies. Recent investigations into natural compounds have identified 8,12-dimethoxysanguinarine (SG-A) from Eomecon chionantha as a potential necroptosis inducer. This study presents the first computational exploration of SG-A interactions with key necroptotic proteins-RIPK1, RIPK3, and MLKL-through molecular docking, molecular dynamics (MD), density functional theory (DFT), and molecular electrostatic potential (MEP) analyses. Molecular docking revealed that SG-A exhibited a stronger affinity for MLKL (-9.40 kcal/mol) compared to the co-crystallized ligand (-6.29 kcal/mol), while its affinity for RIPK1 (-6.37 kcal/mol) and RIPK3 (-7.01 kcal/mol) was lower. MD simulations further demonstrated the stability of SG-A within the MLKL site, with RMSD values stabilizing between 1.4 and 3.3 Å over 300 ns, indicating a consistent interaction pattern. RMSF analysis indicated the preservation of protein backbone flexibility, with average fluctuations under 1.7 Å. The radius of gyration (Rg) results indicated a consistent value of ~15.3 Å across systems, confirming the role of SG-A in maintaining protein integrity. Notably, SG-A maintains two critical H-bonds within the active site of MLKL, reinforcing the stability of the interaction. Principal component analysis (PCA) indicated a significant reduction in MLKL's conformational space upon SG-A binding, implying enhanced stabilization. Dynamic cross-correlation map (DCCM) analysis further revealed that SG-A induced highly correlated motions, reducing internal fluctuations within MLKL compared to the co-crystallized ligand. MM-PBSA revealed the enhanced binding efficacy of SG-A, with a significant binding free energy of -31.03 ± 0.16 kcal/mol against MLKL, surpassing that of the control (23.96 ± 0.11 kcal/mol). In addition, the individual residue contribution analysis highlighted key interactions, with ARG149 showing a significant contribution (-176.24 kcal/mol) in the MLKL-SG-A complex. DFT and MEP studies corroborated these findings, revealing that the electronic structure of SG-A is conducive to stable binding interactions, characterized by a narrow band gap (~0.16 units) and distinct electrostatic potential favourable for necroptosis induction. In conclusion, SG-A has emerged as a compelling inducer of necroptosis for breast cancer therapy, warranting further experimental validation to fully realize its therapeutic potential.

撤稿信息
撤稿日期 2026
撤稿期刊 PloS one
发布机构 United States
通知PMID 41973656
撤稿通知标题:
Expression of Concern: Targeting necroptosis in MCF-7 breast cancer cells: In Silico insights into 8,12-dimethoxysanguinarine from Eomecon Chionantha through molecular docking, dynamics, DFT, and MEP studies
AI 提取信息
研究领域
生物信息学
文章类型
原创研究(Original Research)
研究方法
生物信息学分析
疾病/条件
乳腺癌
数据来源
公共数据库(Public Database)
撤稿原因
无法确定
撤稿类型
关注声明(Expression of Concern)
研究机构
Faculty of Pharmacy, Department of Pharmacy, Jadara University, Irbid, Jordan; Michael Sayegh Faculty of Pharmacy, Aqaba University of Technology, Aqaba, Jordan; Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India; Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, India; Faculty of Pharmacy and Biomedical Sciences, Department of Medicinal Chemistry, MAHSA University, Jenjarom, Selangor, Malaysia; Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, Al al-bayt University, Mafraq, Jordan
国家/地区
Jordan; 印度; 马来西亚
资助来源
未提及
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