121
observed with BSA where the top 10 binding modes changed positions dramatically
between docking. Docking runs were performed with two versions of the target polymerase PDB files, one in which the coordinates for the DNA atoms were left in place
(binary form) and the other in which these were removed to give an “apo” form. The
only difference observed in the results obtained with these two versions was in the
number of clusters observed in pocket A.
Unfortunately, information about structural details of Y family pols interaction
with MK886 presented in paper of Ketkar et al. [125] is very poor. The negative impact upon catalysis if MK886 binds to pocket A is obvious for all three polymerases.
In the case of pol ι, the interactions between MK886 and the side chains of Arg103
and Arg331 would disrupt key electrostatic interactions between the polymerase
and the template strand. Similar effects upon DNA binding could be predicted for
pol η and pol κ. Consideration of inhibitor binding to pocket B in pol ι shows that
electrostatic interaction between the docked MK886 molecule and Asn216 stations
the inhibitor near the “gate” to the dNTP binding cleft, which could also reasonably
be assumed to interfere with the productive binding of the incoming nucleotide triphosphate. Likewise, binding of MK886 to pocket B of either pol η or pol κ could
conceivably interfere with the productive dNTP binding. Finally, pocket C is only
observed with pol ι, where MK886 is found to interact with residues in the thumb
and palm domains. The potential inhibitory effect of pocket C is less obvious than
that of either pocket A or pocket B. In pocket C, MK886 interacts with residues that
are near the base of the αH helix (Gln227) in the thumb domain, located not far from
the binding site of the third metal ion. Transient coordination of the third metal ion
was recently shown to play a role in the catalysis by pol η, and metal ion coordination has been suggested to be the rate-limiting step in the catalysis by pol η [130,
131]. Other studies have revealed that conformational changes in the thumb domain
play a role in nucleotide selection by Y family polymerases [132, 133]. Thus, it
would appear that binding of MK886 to pocket C near the pol ι thumb region may
contribute to the more potent inhibitory effect by interfering with either conformational changes or metal ion dynamics and that this effect is not observed for either
pol η and pol κ since they do not possess a well-formed pocket C.
In silico approaches are also used for the analysis of structural insights of bacterial polymerases inhibition. Martin et al. [134] have studied possible structural
mechanisms of Taq polymerase I inhibition by 6,10,2′,6′-tetraacetyl-O-catalpol
(Table 4.2) with the wide spectrum of computational methods. Classical and semiempirical methods were used to characterize the conformational preferences of this
organic compound in solution. The Gabedit software package [135] was used to
generate a catalpol starting geometry which was initially optimized using the classic
quasi-Newton method, followed by semiempirical optimization using the software
MOPAC [136]. Minimized conformation was used to obtain the parameters and
topology files for the GROMACS software [137, 138] using the ProDGR server
[139]. The analysis of catalpol conformational space was performed using two different approaches—simulated annealing (SA) and molecular dynamics (MD). SA
was performed with GROMACS software using appropriate protocol. The force
field used was ffG53a6, the solvent was explicitly simulated using the SPC model,
4 DNA Dependent DNA Polymerases as Targets for Low-Weight …
observed with BSA where the top 10 binding modes changed positions dramatically
between docking. Docking runs were performed with two versions of the target polymerase PDB files, one in which the coordinates for the DNA atoms were left in place
(binary form) and the other in which these were removed to give an “apo” form. The
only difference observed in the results obtained with these two versions was in the
number of clusters observed in pocket A.
Unfortunately, information about structural details of Y family pols interaction
with MK886 presented in paper of Ketkar et al. [125] is very poor. The negative impact upon catalysis if MK886 binds to pocket A is obvious for all three polymerases.
In the case of pol ι, the interactions between MK886 and the side chains of Arg103
and Arg331 would disrupt key electrostatic interactions between the polymerase
and the template strand. Similar effects upon DNA binding could be predicted for
pol η and pol κ. Consideration of inhibitor binding to pocket B in pol ι shows that
electrostatic interaction between the docked MK886 molecule and Asn216 stations
the inhibitor near the “gate” to the dNTP binding cleft, which could also reasonably
be assumed to interfere with the productive binding of the incoming nucleotide triphosphate. Likewise, binding of MK886 to pocket B of either pol η or pol κ could
conceivably interfere with the productive dNTP binding. Finally, pocket C is only
observed with pol ι, where MK886 is found to interact with residues in the thumb
and palm domains. The potential inhibitory effect of pocket C is less obvious than
that of either pocket A or pocket B. In pocket C, MK886 interacts with residues that
are near the base of the αH helix (Gln227) in the thumb domain, located not far from
the binding site of the third metal ion. Transient coordination of the third metal ion
was recently shown to play a role in the catalysis by pol η, and metal ion coordination has been suggested to be the rate-limiting step in the catalysis by pol η [130,
131]. Other studies have revealed that conformational changes in the thumb domain
play a role in nucleotide selection by Y family polymerases [132, 133]. Thus, it
would appear that binding of MK886 to pocket C near the pol ι thumb region may
contribute to the more potent inhibitory effect by interfering with either conformational changes or metal ion dynamics and that this effect is not observed for either
pol η and pol κ since they do not possess a well-formed pocket C.
In silico approaches are also used for the analysis of structural insights of bacterial polymerases inhibition. Martin et al. [134] have studied possible structural
mechanisms of Taq polymerase I inhibition by 6,10,2′,6′-tetraacetyl-O-catalpol
(Table 4.2) with the wide spectrum of computational methods. Classical and semiempirical methods were used to characterize the conformational preferences of this
organic compound in solution. The Gabedit software package [135] was used to
generate a catalpol starting geometry which was initially optimized using the classic
quasi-Newton method, followed by semiempirical optimization using the software
MOPAC [136]. Minimized conformation was used to obtain the parameters and
topology files for the GROMACS software [137, 138] using the ProDGR server
[139]. The analysis of catalpol conformational space was performed using two different approaches—simulated annealing (SA) and molecular dynamics (MD). SA
was performed with GROMACS software using appropriate protocol. The force
field used was ffG53a6, the solvent was explicitly simulated using the SPC model,
4 DNA Dependent DNA Polymerases as Targets for Low-Weight …