Abstract Entecavir, triphosphorylated in liver cells, is an antiviral reagent against Hepatitis B virus (HBV). The reagent inhibits reverse transcription of RNA inside the virus capsid. In the present study, free energy profile of an Entecavir triphosphate (ETVTP) molecule has been calculated when it passes through pores of the capsid along two- and three-fold rotational symmetry axes in order to investigate permeation pathway of the reagent to the inside of the capsid. The calculations have been done based on thermodynamic integration (TI) method combined with all-atomistic molecular dynamic (MD) calculations. A free energy minimum of −19 kJ/mol was found at the entrance of the pore from the outside along the three-fold symmetry axis. This stabilization is from the interaction of negatively charged ETVTP with positively charged capsid methionine residues. This excess free energy concentrates of the reagent at the entrance of the pore by a factor of about 2000. A free energy barrier of approximately 13 kJ/mol was also found near the exit of the pore to the inside of the capsid due to narrow space of the pore surrounded by hydrophobic wall made by proline residues and negatively charged wall by aspartic acid residues. There, ETVTP is partially dehydrated in order to pass through the narrow space, which causes the great free energy loss. Further, the negatively charged residues produce repulsive forces on the ETVTP molecule. In contrast, in the case of the pore along the two-fold symmetry axis, the calculated free energy profile showed shallower free energy minimum, −4 kJ/mol at the entrance in spite of the similarly high barrier, 7 kJ/mol, near the exit of the pore.

中文翻译：

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通过分子动力学计算研究恩替卡韦通过乙型肝炎病毒衣壳渗透的自由能分布

摘要 恩替卡韦在肝细胞中三磷酸化，是一种抗乙型肝炎病毒 (HBV) 的抗病毒试剂。该试剂抑制病毒衣壳内 RNA 的逆转录。在本研究中，计算了恩替卡韦三磷酸 (ETVTP) 分子沿两和三倍旋转对称轴穿过衣壳孔时的自由能分布，以研究试剂渗透到衣壳内部的途径。衣壳。计算是基于热力学积分 (TI) 方法结合全原子分子动力学 (MD) 计算完成的。在孔隙入口处沿三重对称轴从外侧发现自由能最小值为 -19 kJ/mol。这种稳定来自带负电的 ETVTP 与带正电的衣壳蛋氨酸残基的相互作用。这种过量的自由能将试剂在孔入口处浓缩了大约 2000 倍。由于空间狭窄，在孔出口附近也发现了约 13 kJ/mol 的自由能垒。由脯氨酸残基构成的疏水壁和由天冬氨酸残基构成的带负电荷的壁包围的孔。在那里，ETVTP为了通过狭窄的空间而部分脱水，这造成了很大的自由能损失。此外，带负电荷的残基对 ETVTP 分子产生排斥力。相比之下，在孔沿双重对称轴的情况下，计算的自由能分布显示更浅的自由能最小值，