Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation

Kazushi Fujimoto, Motohiro Fukai, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, Susumu Okazaki

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2 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1585-1594
Number of pages10
JournalPure and Applied Chemistry
Issue number10
Publication statusPublished - Oct 1 2020
Externally publishedYes


  • Entecavir
  • free energy, Hepatitis B virus
  • ICSC-36
  • molecular dynamics calculation

ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)


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