model structure but a modification of an X-ray, the docking protocol was still able to
identify several validated hit compounds. It is a common situation with many highaffinity compounds that the protein-ligand complex is highly complementary. In
such a case, docking is often unable to produce a proper binding pose for inhibitors
which are structurally different from the inhibitor within the X-ray structure. As an
example, one can look at the data from Pedreira et al., in which both normal docking
and induced-fit docking approaches were unable to create proper binding modes for
type 1.5 p38alfa MAP kinase inhibitors [26]. Only after manual modification of
kinase conformation, a proper binding pose was constructed. This pose was validated by long MD simulations (3.6 μs) with three replicas for all studied systems.
Unlike in many other modeling studies in which MD simulations are used to support
the docking results, this extremely long MD simulation is truly validating the
proposed docking poses. One cannot claim the same for those cases where MD
simulation is either only single run and/or clearly shorter than 500–1,000 ns, as that
timescale is just enough to cover protein side chain movements or so-called tier
1 movements [27, 28].
One additional point to discuss is related to the idea of targeting inactive kinase
conformation. The question is if all DFG-in structures are also catalytically active
kinase structures or if there are DFG-in-like structures which are catalytically
inactive. It seems that this is the case, as a quite recent paper by Modi and Dunbrack
[23] nicely demonstrates that only a small part of DFG-in conformations is catalytically active. To be catalytically active, the protein kinase should have all the
structural features required for phosphorylation activity, including a proper setup
to accommodate the ATP molecule and the magnesium ion. Indeed, there are several
X-ray structures with DFG-in-like features but without proper conformation to
accommodate the ATP and the metal ion. What is not known at the moment is
whether these inactive DFG-in-like structures are thermodynamically distinct ones
in vivo and thus biologically valid or whether the inactive DFG-in structures are just
artifacts of the crystallization conditions. Current data indicate that the first option is
valid, as combination of X-ray structure analysis and long-scale MD simulations
with CDK2 was able to identify not only classical active and inactive kinase
conformations but also several metastable states [29].
3 MD Simulations
As one can see, MD simulations are becoming an increasingly popular research tool
to study both conformational aspects of protein kinases and for understanding drugprotein interactions. There are several factors which are making MD a true option,
but the most important ones are the dramatically increased performance due to GPU
implementation of software, better force fields, and especially the Markov State
Modeling approach [30]. Around 10 years ago, most of the published MD simulations included at maximum 1 μs simulation time, but current studies can easily be
based on data from an over 1 ms timeframe [31]. In our group, a routine simulation
Molecular Modeling of Protein Kinases: Current Status and Challenges
31
identify several validated hit compounds. It is a common situation with many highaffinity compounds that the protein-ligand complex is highly complementary. In
such a case, docking is often unable to produce a proper binding pose for inhibitors
which are structurally different from the inhibitor within the X-ray structure. As an
example, one can look at the data from Pedreira et al., in which both normal docking
and induced-fit docking approaches were unable to create proper binding modes for
type 1.5 p38alfa MAP kinase inhibitors [26]. Only after manual modification of
kinase conformation, a proper binding pose was constructed. This pose was validated by long MD simulations (3.6 μs) with three replicas for all studied systems.
Unlike in many other modeling studies in which MD simulations are used to support
the docking results, this extremely long MD simulation is truly validating the
proposed docking poses. One cannot claim the same for those cases where MD
simulation is either only single run and/or clearly shorter than 500–1,000 ns, as that
timescale is just enough to cover protein side chain movements or so-called tier
1 movements [27, 28].
One additional point to discuss is related to the idea of targeting inactive kinase
conformation. The question is if all DFG-in structures are also catalytically active
kinase structures or if there are DFG-in-like structures which are catalytically
inactive. It seems that this is the case, as a quite recent paper by Modi and Dunbrack
[23] nicely demonstrates that only a small part of DFG-in conformations is catalytically active. To be catalytically active, the protein kinase should have all the
structural features required for phosphorylation activity, including a proper setup
to accommodate the ATP molecule and the magnesium ion. Indeed, there are several
X-ray structures with DFG-in-like features but without proper conformation to
accommodate the ATP and the metal ion. What is not known at the moment is
whether these inactive DFG-in-like structures are thermodynamically distinct ones
in vivo and thus biologically valid or whether the inactive DFG-in structures are just
artifacts of the crystallization conditions. Current data indicate that the first option is
valid, as combination of X-ray structure analysis and long-scale MD simulations
with CDK2 was able to identify not only classical active and inactive kinase
conformations but also several metastable states [29].
3 MD Simulations
As one can see, MD simulations are becoming an increasingly popular research tool
to study both conformational aspects of protein kinases and for understanding drugprotein interactions. There are several factors which are making MD a true option,
but the most important ones are the dramatically increased performance due to GPU
implementation of software, better force fields, and especially the Markov State
Modeling approach [30]. Around 10 years ago, most of the published MD simulations included at maximum 1 μs simulation time, but current studies can easily be
based on data from an over 1 ms timeframe [31]. In our group, a routine simulation
Molecular Modeling of Protein Kinases: Current Status and Challenges
31