木犀草素抑制肝纤维化关键蛋白PTK2的分子机制：基于分子对接与动力学模拟的研究

Molecular Mechanism of Luteolin’s Inhibition of PTK2, a Key Protein in Liver Fibrosis: A Study Based on Molecular Dynamics Simulation

摘要: 目的：本研究旨在通过计算模拟方法，探究叶下珠的主要活性成分之一木犀草素与肝纤维化相关蛋白蛋白酪氨酸激酶2(PTK2)之间的相互作用机制，评估其作为PTK2抑制剂的潜力。方法：采用分子对接技术预测木犀草素与PTK2的最佳结合模式与亲和力；进而利用分子动力学模拟评估复合物在100 ns内的结构稳定性、动力学行为及关键相互作用；最后通过MM-PBSA方法计算结合自由能并进行残基能量分解分析。结果：分子对接显示木犀草素与PTK2具有高亲和力(最佳结合能为−8.0 kcal/mol)，并稳定结合于其活性口袋。分子动力学模拟表明，复合物结构稳定，木犀草素在结合口袋内无显著位移。结合自由能计算(ΔG_bind = −68.815 kJ/mol)证实结合为自发过程，且能量分解揭示结合主要由范德华力(疏水相互作用)驱动，并辅以关键的氢键网络。残基贡献分析进一步识别出ILE-428、LEU-553和CYS-502等为关键“热点”残基。结论：理论计算预测表明，木犀草素能够通过与PTK2活性口袋形成稳定复合物而高效抑制其活性，这为阐释木犀草素的抗肝纤维化作用机制提供了分子水平依据，并为其作为先导化合物的优化提示了方向。

Abstract: Objective: This study aimed to investigate the interaction mechanism between luteolin, one of the primary active components of Phyllanthus urinaria, and Protein Tyrosine Kinase 2 (PTK2), a protein associated with liver fibrosis, using computational simulation methods, and to evaluate its potential as a PTK2 inhibitor. Methods: Molecular docking was employed to predict the optimal binding mode and affinity between luteolin and PTK2. Subsequently, Molecular Dynamics (MD) simulations were used to assess the structural stability, dynamic behavior, and key interactions of the complex over 100 ns. Finally, the binding free energy was calculated using the MM-PBSA method, followed by per-residue energy decomposition analysis. Results: Molecular docking revealed that luteolin exhibits high affinity (optimal binding energy: −8.0 kcal/mol) for PTK2 and stably binds within its active pocket. MD simulations indicated that the complex structure remained stable, with no significant displacement of luteolin within the binding pocket. The binding free energy calculation (ΔG_bind = −68.815 kJ/mol) confirmed that the binding is a spontaneous process. Energy decomposition revealed that the binding is primarily driven by van der Waals forces (hydrophobic interactions), supplemented by a critical hydrogen bond network. Per-residue energy contribution analysis further identified ILE-428, LEU-553, and CYS-502 as key “hotspot” residues. Conclusion: Theoretical calculations predict that luteolin can effectively inhibit PTK2 activity by forming a stable complex with its active pocket. This provides a molecular-level basis for explaining luteolin’s anti-hepatic fibrosis mechanism and suggests directions for optimizing it as a lead compound.