School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia.
Chemphyschem. 2021 Mar 3;22(5):493-498. doi: 10.1002/cphc.202000873. Epub 2021 Feb 1.
Cell-penetrating peptides are used in the delivery of peptides and biologics, with some cell-penetrating peptides found to be more efficient than others. The exact mechanism of how they interact with the cell membrane and penetrate it, however, remains unclear. This study attempts to investigate the difference in free energy profiles of three cell-penetrating peptides (TAT, CPP1 and CPP9) with a model lipid bilayer (DOPC) using molecular dynamics pulling simulations with umbrella sampling. Potential mean force (PMF) and free energy barrier between the peptides and DOPC are determined using WHAM analysis and MM-PBSA analysis, respectively. CPP9 is found to have the smallest PMF value, followed by CPP1 and TAT, consistent with the experimental data. YDEGE peptide, however, does not give the highest PMF value, although it is a non-cell-permeable peptide. YDEGE is also found to form water pores, alongside with TAT and CPP9, suggesting that it is difficult to distinguish true water pore formation from artefacts arising from pulling simulations. On the contrary, free energy analysis of the peptide-DOPC complex at the lipid-water interface with MM-PBSA provides results consistent with experimental data with CPP9 having the least interaction with DOPC and lowest free energy barrier, followed by CPP1, TAT and YDEGE. These findings suggest that peptide-lipid interaction at the lipid-water interface has a direct correlation with the penetration efficiency of peptides across the lipid bilayer.
细胞穿透肽被用于肽类和生物制剂的递送，一些细胞穿透肽被发现比其他肽类更有效。然而，它们与细胞膜相互作用并穿透细胞膜的确切机制仍不清楚。本研究试图使用分子动力学牵引模拟和伞状采样，研究三种细胞穿透肽（TAT、CPP1 和 CPP9）与模型脂质双层（DOPC）之间的自由能谱差异。使用 WHAM 分析和 MM-PBSA 分析分别确定肽和 DOPC 之间的势平均力（PMF）和自由能势垒。CPP9 具有最小的 PMF 值，其次是 CPP1 和 TAT，这与实验数据一致。然而，YDEGE 肽尽管是一种非细胞穿透肽，但并没有给出最高的 PMF 值。YDEGE 还与 TAT 和 CPP9 一起形成水孔，表明很难将真正的水孔形成与牵引模拟产生的假象区分开来。相反，使用 MM-PBSA 对位于脂质-水界面的肽-DOPC 复合物进行自由能分析，得到的结果与实验数据一致，CPP9 与 DOPC 的相互作用最小，自由能势垒最低，其次是 CPP1、TAT 和 YDEGE。这些发现表明，肽-脂质在脂质-水界面的相互作用与肽穿过脂质双层的穿透效率直接相关。
