Binding sensitivity of adefovir to the polymerase from different genotypes of HBV: molecular modeling, docking and dynamics simulation studies

Abstract

Aim: To investigate the molecular mechanisms underlying the influence of DNA polymerase from different genotypes of hepatitis B virus (HBV) on the binding affinity of adefovir (ADV).

Methods: Computational approaches, including homology modeling, docking, MD simulation and MM/PBSA free energy analyses were used.

Results: Sequence analyses revealed that residue 238 near the binding pocket was not only a polymorphic site but also a genotype-specific site (His238 in genotype B; Asn238 in genotype C). The calculated binding free-energy supported the hypothesis that the polymerase from HBV genotype C was more sensitive to ADV than that from genotype B. By using MD simulation trajectory analysis, binding free energy decomposition and alanine scanning, some energy variation in the residues around the binding pocket was observed. Both the alanine mutations at residues 236 and 238 led to an increase of the energy difference between genotypes C and B (ΔΔG(C-B)), suggesting that these residues contributed to the genotype-associated antiviral variability with regard to the interaction with ADV.

Conclusion: The results support the hypothesis that the HBV genotype C polymerase is more sensitive to ADV than that from genotype B. Moreover, residue N236 and the polymorphic site 238 play important roles in contributing to the higher sensitivity of genotype C over B in the interaction with ADV.

Figure 1

Chemical structures of five nucleotide analogue HBV polymerase inhibitor approved by US-FDA for treatment of HBV infection.

Figure 2

Alignment of HBV polymerase and HIV-1 RT sequences showing the identical (dark shaded) and closely related (light shaded) residues.

Figure 3

(A) Overall view of superposition of template structure 1T05 (magenta ribbon) with HBV polymerase genotype B (cyan) and C (green) model structures from homology modeling, ligand ADV-DP and two Mg²⁺ ions are highlighted in magenta and gray. (B) The 3D structural model of finger, palm, and thumb subdomains in HBV polymerase are represented in green, blue and salmon ribbons, respectively. DNA template-primer duplex is shown in orange cartoon mode. (C) The structurally conserved catalytic subdomains are displayed in colored ribbons: Domains A (cyan), B (yellow), C (pink), D (green), E (blue), F (magenta), and G (marine).

Figure 4

Binding modes of: (A) HBV polymerase genotype B and (B) genotype C with ADV-DP. Two Mg²⁺ ions are shown in gray colored spheres. The ligand ADV-DP is shown in magenta colored ball-and-stick mode. Mg²⁺ coordination and hydrogen bond interactions are shown with black dotted lines.

Figure 5

Root mean squared deviation (RMSD) of HBV polymerase homology model during the molecular dynamics simulation with respect to its starting (docked) pose.

Figure 6

Distance graphs of some important hydrogen bonding interactions. Two maintained hydrogen bonds: (a) between N1 of ADV-DP and NH of dTMP; (b) and between NH₂ of ADV-DP and carbonyl O of dTMP. Panel (c) shows distance variations between α-phosphate of ADV-DP and the residue Arg41. (d) The residue Ser85 was distant in the beginning of the MD simulation; loop movement pushed the side chain amide toward the γ-phosphate of ADV-DP as described. (e) Distances between the hydroxyl group of Ser85 and NH₂ of Asn236. (A) Genotype B; (B) Genotype C.

Figure 7

Decomposition of binding energy (GBTOT) on a per-residue basis, only residues making significant favorable or unfavorable contribution were shown (|GBTOT|≥1.0 kcal/mol).