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. 2014 May 5;9(5):e96789.
doi: 10.1371/journal.pone.0096789. eCollection 2014.

Evaluation of influence of single nucleotide polymorphisms in cytochrome P450 2B6 on substrate recognition using computational docking and molecular dynamics simulation

Kana Kobayashi  1 , Ohgi Takahashi  1 , Masahiro Hiratsuka  2 , Noriyuki Yamaotsu  3 , Shuichi Hirono  3 , Yurie Watanabe  4 , Akifumi Oda  5
Affiliations

Evaluation of influence of single nucleotide polymorphisms in cytochrome P450 2B6 on substrate recognition using computational docking and molecular dynamics simulation

Kana Kobayashi et al. PLoS One. .

Abstract

In this study, we investigated the influence of single nucleotide polymorphisms on the conformation of mutated cytochrome P450 (CYP) 2B6 proteins using molecular dynamics (MD) simulation. Some of these mutations influence drug metabolism activities, leading to individual variations in drug efficacy and pharmacokinetics. Using computational docking, we predicted the structure of the complex between the antimalarial agent artemether and CYP2B6 whose conformations were obtained by MD simulation. The simulation demonstrated that the entire structure of the protein changes even when a single residue is mutated. Moreover, the structural flexibility is affected by the mutations and it may influence the enzyme activity. The results suggest that some of the inactive mutants cannot recognize artemether due to structural changes caused by the mutation.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Structure of AM.
The position demethylated by CYP is indicated by a dashed line.
Figure 2
Figure 2. RMSDs for two mutants of CYP2B6.
RMSD of CYP2B6.4 (A) converged, whereas that of CYP2B6.12 (B) did not converge at 20 ns.
Figure 3
Figure 3. RMSF of the Cα atoms in the wild-type.
The highest peak was Thr255. Around the highest peak, there are RMSF peaks at those for Tyr226 and Ala279. An additional peak is observed at the peak for Asn417.
Figure 4
Figure 4. RMSFs of the Cα atoms in mutants.
(A) CYP2B6.4, (B) CYP2B6.8, (C) CYP2B6.11, (D) CYP2B6.12, (E) CYP2B6. 15, (F) CYP2B6. 18, (G) CYP2B6.21, and (H) CYP2B6.24. In some mutants, the locations and heights of the peaks are different from those in the wild-type. A prominent peak is observed at 100–200th residues in some mutants but not in the wild-type.
Figure 5
Figure 5. The structure of CYP2B6 shown by a ribbon diagram.
The helices near the substrate recognition site, C, I, and L helices, are shown in purple.
Figure 6
Figure 6. Ribbon-and-stick diagram showing the C/D loop (yellow) and the G/H loop (purple).
(A) CYP2B6.8. (B) CYP2B6.11. The relative position of the C/D and the G/H loop differs dramatically among mutants.
Figure 7
Figure 7. Ribbon-and-stick diagram showing the I helix and the heme of the CYP2B6 wild-type (blue) and CYP2B6.12 variant (purple).
Figure 8
Figure 8. CYP2B6.1 and CYP2B6.8 colored for isotropic displacement.
The larger value of the isotropic displacement is indicated by red.
Figure 9
Figure 9. Structure of the complex between the wild-type and AM after docking simulation.
(A) The whole complex structure. CYP2B6.1 is shown by ribbon, heme and AM are shown by ball-and-stick representation. AM is circled. (B) Structure around the active site. The residues of CYP2B6.1 are shown by stick, heme and AM are shown by ball-and-stick representation.
Figure 10
Figure 10. Structure of the helices around the heme.
The C, D, E, G, H, and I helices of the CYP2B6 wild-type (blue) and CYP2B6.18 variant (purple) are shown by ribbons; the heme is shown by ball-and-stick representation.
Figure 11
Figure 11. Ligand binding pocket of CYP2B6.18 detected by HBOP and HBSITE.
The binding pocket is illustrated by probe spheres.
Figure 12
Figure 12. Hydrogen bond between AM and Thr302 in CYP2B6.8.
Figure 13
Figure 13. Ligand binding pockets of CYP2B6.1 (light blue) and CYP2B6.4 (brown).
The pockets is illustrated by probe spheres.
See this image and copyright information in PMC

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