124
group of ADV-DP. Arg41 in the systems of genotypes B and C formed three and two
hydrogen bonds with ADV-DP, respectively. The carbonyl groups of Asp83, Asp205
and Val84 together with the three phosphate groups of ADV-DP formed a metal chelating interaction with the two Mg
2+
ions that were present in the active site [145].
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 for the HBV pol from
genotypes C and B is − 147.81 and − 126.85 kcal/mol, respectively. It confirms the
hypothesis that the HBV pol from genotype C is more sensitive to the ADV treatment than one from genotype B. By using the MD simulation trajectory analysis and binding free energy decomposition, some energy variation in the residues
around the binding pocket was observed. According to the energy decomposition
data, residues Lys32, Arg41, Asp83, Ser85, Ala86, Ala87 and dTMP make a main
contribution into the ADV-DP binding, due to the hydrogen bonding. The purine
ring of ADV-DP formed a strong π–π stacking interaction with the primer DNA
base, which also showed an obvious hydrophobic interaction with Phe88. Phe88
is located within the hydrophobic pocket comprised of Ala87, Phe88, Ile180, and
Met204. This result is consistent with the report by Daga et al. [155]. In addition, for
most of the key residues, a slightly stronger binding energy contribution was found
in the genotype C system [145].
Thus, investigations of structural insights of pol–inhibitor interaction have received a substantial boost during the last years, which provides the opportunity to
use their results in rational design of new compounds with directed antipolymerases
activity.
4.5 Computational Approaches in Rational Design
of DNA Polymerase Inhibitors
Modern strategies of rational design of specific/selective effectors for biomolecular targets naturally combine the computational approaches, used for the detailed
analysis of the structural mechanisms of ligand–target interaction, and predictions
of the ligand affinity with instrumental methods of activity and selectivity assessment for the developed compounds [156]. Actually, the rational design procedure
consists of the following steps:
• the choice of a biomolecular target (protein in the most common case);
• the analysis of individual spatial structure features of the functional and allosteric sites of the target protein;
• high throughput receptor-based virtual screening of libraries of low-weight molecular organic compounds, and identification of classes of compounds characterized by the highest affinity to the target protein in silico;
• experimental verification of the inhibitory activity and selectivity of the most
promising compounds according to the previous stage on set close to the target
protein in vitro;
A. Yu. Nyporko
group of ADV-DP. Arg41 in the systems of genotypes B and C formed three and two
hydrogen bonds with ADV-DP, respectively. The carbonyl groups of Asp83, Asp205
and Val84 together with the three phosphate groups of ADV-DP formed a metal chelating interaction with the two Mg
2+
ions that were present in the active site [145].
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 for the HBV pol from
genotypes C and B is − 147.81 and − 126.85 kcal/mol, respectively. It confirms the
hypothesis that the HBV pol from genotype C is more sensitive to the ADV treatment than one from genotype B. By using the MD simulation trajectory analysis and binding free energy decomposition, some energy variation in the residues
around the binding pocket was observed. According to the energy decomposition
data, residues Lys32, Arg41, Asp83, Ser85, Ala86, Ala87 and dTMP make a main
contribution into the ADV-DP binding, due to the hydrogen bonding. The purine
ring of ADV-DP formed a strong π–π stacking interaction with the primer DNA
base, which also showed an obvious hydrophobic interaction with Phe88. Phe88
is located within the hydrophobic pocket comprised of Ala87, Phe88, Ile180, and
Met204. This result is consistent with the report by Daga et al. [155]. In addition, for
most of the key residues, a slightly stronger binding energy contribution was found
in the genotype C system [145].
Thus, investigations of structural insights of pol–inhibitor interaction have received a substantial boost during the last years, which provides the opportunity to
use their results in rational design of new compounds with directed antipolymerases
activity.
4.5 Computational Approaches in Rational Design
of DNA Polymerase Inhibitors
Modern strategies of rational design of specific/selective effectors for biomolecular targets naturally combine the computational approaches, used for the detailed
analysis of the structural mechanisms of ligand–target interaction, and predictions
of the ligand affinity with instrumental methods of activity and selectivity assessment for the developed compounds [156]. Actually, the rational design procedure
consists of the following steps:
• the choice of a biomolecular target (protein in the most common case);
• the analysis of individual spatial structure features of the functional and allosteric sites of the target protein;
• high throughput receptor-based virtual screening of libraries of low-weight molecular organic compounds, and identification of classes of compounds characterized by the highest affinity to the target protein in silico;
• experimental verification of the inhibitory activity and selectivity of the most
promising compounds according to the previous stage on set close to the target
protein in vitro;
A. Yu. Nyporko