several other molecule methods. Although it is not mandatory, validation of the
docking pose would increase the value of the study [17]. One simple approach was
used by Ortuso et al. who combined several docking results (Glide XP) from X-ray
structures of the Sgk1 kinase [18]. This approach yielded an average docking score
which was used to identify a sub-micromolar Sgk1 inhibitor. Many research groups
have used more complicated approaches and combined docking with binding free
energy calculations and/or QSAR [19] or used a sequential approach with
pharmacophore pre-screening before docking with different methods [20]. It is
seldom that docking is used alone, and typically, docking is combined with one or
several other modeling and screening methods. The reason for this complexity is
quite simple: scoring functions are far from optimal, and typical docking results
include a high number of false-positive and false-negative “hits” [12]. Due to this,
kinase-specific scoring functions or rescoring have also been used resulting in the
identification of a sub-micromolar FGFR1 inhibitor [21].
As mentioned above, the DFG domain conformation indicates if the kinase is in
an active or inactive state. This DFG-domain description raises some questions that
should be considered when carrying out virtual screening. The most important one is
quite simple: Should we target DFG-in or DFG-out or some other conformations?
Naturally, the simplest approach is to use whatever empirical structure is available.
This is a valid option if one is ready to accept any type of inhibitor as a result. In
many cases, researchers are more interested to find either type II or type 1½ inhibitor,
especially, since it has been stated that better selectivity is reached if inactive kinase
conformation is targeted [22]. As most of the empirical kinase structures are the
DFG-in type [23], targeting inactive kinase conformation is not automatically an
option. In theory, one can modify the kinase structure and use, for example,
homology modeling or MD simulations to produce a DFG-out structure by using a
catalytically active DFG-in conformation as a starting point. In practice, this
approach is difficult to use and requires a substantial amount of pre-existing structural data [24]. Docking itself is a static approach, and structural errors outside of the
protein binding site do not affect the outcome. Thus, one should be able to get viable
results if the binding cavity itself has an appropriate conformation. This is probably
also valid for induced-fit docking methods, if the used method is not based on MD
simulations. However, one cannot use a classical MD-ensemble docking if the
kinase structure has structural issues anywhere near the binding site, since those
errors would easily be reflected to the binding site of the protein kinase.
One way to modify the kinase structure is to use an induced-fit protocol and
modify the target kinase conformation so that structural features are as required. This
approach was used to identify inhibitors against zeta-chain protein kinase 70 kDa
(ZAP70) [25]. The gatekeeper residue methionine 414 was modified to resemble the
structure of Janus kinase 2 (JAK2) by aligning ZAP70 to JAK2 binding sites. In
addition, a potent JAK2 inhibitor was docked to the resulting structure, and the
ZAP70/JAK2-inhibitor complex was relaxed by MD simulation procedure. The
induced-fit ZAP70 structure was used for the docking campaign, and several low
and sub-micromolar ZAP70 inhibitors were identified. This protocol proves that
although the structure used for the docking campaign was not a classical homology
30
A. Poso
docking pose would increase the value of the study [17]. One simple approach was
used by Ortuso et al. who combined several docking results (Glide XP) from X-ray
structures of the Sgk1 kinase [18]. This approach yielded an average docking score
which was used to identify a sub-micromolar Sgk1 inhibitor. Many research groups
have used more complicated approaches and combined docking with binding free
energy calculations and/or QSAR [19] or used a sequential approach with
pharmacophore pre-screening before docking with different methods [20]. It is
seldom that docking is used alone, and typically, docking is combined with one or
several other modeling and screening methods. The reason for this complexity is
quite simple: scoring functions are far from optimal, and typical docking results
include a high number of false-positive and false-negative “hits” [12]. Due to this,
kinase-specific scoring functions or rescoring have also been used resulting in the
identification of a sub-micromolar FGFR1 inhibitor [21].
As mentioned above, the DFG domain conformation indicates if the kinase is in
an active or inactive state. This DFG-domain description raises some questions that
should be considered when carrying out virtual screening. The most important one is
quite simple: Should we target DFG-in or DFG-out or some other conformations?
Naturally, the simplest approach is to use whatever empirical structure is available.
This is a valid option if one is ready to accept any type of inhibitor as a result. In
many cases, researchers are more interested to find either type II or type 1½ inhibitor,
especially, since it has been stated that better selectivity is reached if inactive kinase
conformation is targeted [22]. As most of the empirical kinase structures are the
DFG-in type [23], targeting inactive kinase conformation is not automatically an
option. In theory, one can modify the kinase structure and use, for example,
homology modeling or MD simulations to produce a DFG-out structure by using a
catalytically active DFG-in conformation as a starting point. In practice, this
approach is difficult to use and requires a substantial amount of pre-existing structural data [24]. Docking itself is a static approach, and structural errors outside of the
protein binding site do not affect the outcome. Thus, one should be able to get viable
results if the binding cavity itself has an appropriate conformation. This is probably
also valid for induced-fit docking methods, if the used method is not based on MD
simulations. However, one cannot use a classical MD-ensemble docking if the
kinase structure has structural issues anywhere near the binding site, since those
errors would easily be reflected to the binding site of the protein kinase.
One way to modify the kinase structure is to use an induced-fit protocol and
modify the target kinase conformation so that structural features are as required. This
approach was used to identify inhibitors against zeta-chain protein kinase 70 kDa
(ZAP70) [25]. The gatekeeper residue methionine 414 was modified to resemble the
structure of Janus kinase 2 (JAK2) by aligning ZAP70 to JAK2 binding sites. In
addition, a potent JAK2 inhibitor was docked to the resulting structure, and the
ZAP70/JAK2-inhibitor complex was relaxed by MD simulation procedure. The
induced-fit ZAP70 structure was used for the docking campaign, and several low
and sub-micromolar ZAP70 inhibitors were identified. This protocol proves that
although the structure used for the docking campaign was not a classical homology
30
A. Poso