Alhawarri Maram B, Al-Thiabat Mohammad G, Dubey Amit, Tufail Aisha, Banisalman Katreen, Al Jabal Ghazi A, Alkasasbeh Eman, Al-Trad Esra'a Ibrahim, Alrimawi Bilal Harieth
Faculty of Pharmacy, Department of Pharmacy, Jadara University, Irbid, Jordan.
Michael Sayegh Faculty of Pharmacy, Aqaba University of Technology, Aqaba, Jordan.
PLoS One. 2025 Jan 7;20(1):e0313094. doi: 10.1371/journal.pone.0313094. eCollection 2025.
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.
乳腺癌仍然是肿瘤学中的一项重大挑战，这凸显了开发替代治疗策略的必要性，这些策略靶向坏死性凋亡以克服对传统疗法的耐药性。最近对天然化合物的研究已将来自血水草的8,12 - 二甲氧基血根碱（SG - A）鉴定为一种潜在的坏死性凋亡诱导剂。本研究通过分子对接、分子动力学（MD）、密度泛函理论（DFT）和分子静电势（MEP）分析，首次对SG - A与关键坏死性凋亡蛋白RIPK1、RIPK3和MLKL的相互作用进行了计算探索。分子对接显示，与共结晶配体（-6.29 kcal/mol）相比，SG - A对MLKL表现出更强的亲和力（-9.40 kcal/mol），而其对RIPK1（-6.37 kcal/mol）和RIPK3（-7.01 kcal/mol）的亲和力较低。MD模拟进一步证明了SG - A在MLKL位点内的稳定性，在300 ns内RMSD值稳定在1.4至3.3 Å之间，表明存在一致的相互作用模式。RMSF分析表明蛋白质主链柔韧性得以保留，平均波动在1.7 Å以下。回转半径（Rg）结果表明各系统的值一致，约为15.3 Å，证实了SG - A在维持蛋白质完整性方面的作用。值得注意的是，SG - A在MLKL活性位点内维持两个关键氢键，增强了相互作用的稳定性。主成分分析（PCA）表明，SG - A结合后MLKL的构象空间显著减小，意味着稳定性增强。动态交叉相关图（DCCM）分析进一步表明，与共结晶配体相比，SG - A诱导了高度相关的运动，减少了MLKL内部的波动。MM - PBSA显示SG - A具有增强的结合效力，与MLKL的结合自由能显著为-31.03±0.16 kcal/mol，超过了对照（23.96±0.11 kcal/mol）。此外，单个残基贡献分析突出了关键相互作用，在MLKL - SG - A复合物中，ARG149显示出显著贡献（-176.24 kcal/mol）。DFT和MEP研究证实了这些发现，揭示了SG - A的电子结构有利于稳定的结合相互作用，其特征在于窄带隙（约0.16单位）和有利于坏死性凋亡诱导的独特静电势。总之，SG - A已成为一种引人注目的乳腺癌坏死性凋亡诱导剂，需要进一步的实验验证以充分实现其治疗潜力。
