catalytically active DFG-in (type I), all the structure-based modeling methods will
ultimately yield false results. The true issue is the fact that the kinase inhibitor
structure alone is not enough to predict if the inhibitor is type I, II, or something else.
Also very minor changes to the inhibitor structure might change the conformation of
the target kinase [11].
2 Virtual Screening and Docking
Docking is the most commonly used tool in virtual screening. In the case of kinase
inhibitors, one can easily find tens if not hundreds of publications showing different
types of docking approaches used. There is indeed a large number of different
software packages and scoring functions to choose from (for a recent review about
docking in general and especially about the pitfalls, see Pantsar and Poso [12]), but
one cannot claim that any specific method would be clearly better than another. This
does not mean that all the approaches are working or that it doesn’t matter how
virtual screening is carried out [13]. Maybe one of the most critical aspects in
molecular modeling of kinases is the selection of protein kinase conformations to
be used in virtual screening. Kinases are well-known enzymes, and thus conformational variation has been extensively studied [14]. The main way to classify kinase
structures is to use DFG-in and DFG-out families, which refer to the DFG domain
orientation [15]. Although DFG-in and DFG-out are also well explained elsewhere
in this book, it is good to look at the definition on a general level.
The activation loop of the kinase protein controls the enzymatic activity by
relocating itself onto the surface of the protein, resulting in kinase inactivation.
Additional activity control is reached by the DFG motif conformational shifts, so
that the phenylalanine of DFG occupies the ATP binding pocket, and catalytically
active aspartate is pointing away from the active site. In a catalytically active state,
the kinase is always in DFG-in conformation binding the magnesium ion that
interacts directly with an oxygen atom of the β phosphate of ATP. In addition, the
active state includes glutamate from the C-helix in a salt bridge with a lysine of the
β3 strand. This salt bridge stabilizes the hydrogen bonds between lysine and oxygen
atoms of the α and β phosphates of ATP [15].
When we look at the most recent molecular modeling studies where docking has
been used for kinase inhibitor design, we only consider those studies where docking
has been validated either by biological (in vitro) assays or/and X-ray crystallography. It is mandatory that if modeling data are published, and especially if there are
predictions concerning a specific compound, these predictions must be supported by
empirical data. In such a case where modeling is used to make and publish detailed
activity predictions, it will create a situation where the given compounds, even the
hypothetical ones, cannot be protected by patents.
Docking is basically just a method to create and score a protein-ligand binding
pose. Indeed, the simplest way to use docking is to estimate a single compound
binding mode like in the work of Lee et al. [16], which utilized docking together with
Molecular Modeling of Protein Kinases: Current Status and Challenges
29
ultimately yield false results. The true issue is the fact that the kinase inhibitor
structure alone is not enough to predict if the inhibitor is type I, II, or something else.
Also very minor changes to the inhibitor structure might change the conformation of
the target kinase [11].
2 Virtual Screening and Docking
Docking is the most commonly used tool in virtual screening. In the case of kinase
inhibitors, one can easily find tens if not hundreds of publications showing different
types of docking approaches used. There is indeed a large number of different
software packages and scoring functions to choose from (for a recent review about
docking in general and especially about the pitfalls, see Pantsar and Poso [12]), but
one cannot claim that any specific method would be clearly better than another. This
does not mean that all the approaches are working or that it doesn’t matter how
virtual screening is carried out [13]. Maybe one of the most critical aspects in
molecular modeling of kinases is the selection of protein kinase conformations to
be used in virtual screening. Kinases are well-known enzymes, and thus conformational variation has been extensively studied [14]. The main way to classify kinase
structures is to use DFG-in and DFG-out families, which refer to the DFG domain
orientation [15]. Although DFG-in and DFG-out are also well explained elsewhere
in this book, it is good to look at the definition on a general level.
The activation loop of the kinase protein controls the enzymatic activity by
relocating itself onto the surface of the protein, resulting in kinase inactivation.
Additional activity control is reached by the DFG motif conformational shifts, so
that the phenylalanine of DFG occupies the ATP binding pocket, and catalytically
active aspartate is pointing away from the active site. In a catalytically active state,
the kinase is always in DFG-in conformation binding the magnesium ion that
interacts directly with an oxygen atom of the β phosphate of ATP. In addition, the
active state includes glutamate from the C-helix in a salt bridge with a lysine of the
β3 strand. This salt bridge stabilizes the hydrogen bonds between lysine and oxygen
atoms of the α and β phosphates of ATP [15].
When we look at the most recent molecular modeling studies where docking has
been used for kinase inhibitor design, we only consider those studies where docking
has been validated either by biological (in vitro) assays or/and X-ray crystallography. It is mandatory that if modeling data are published, and especially if there are
predictions concerning a specific compound, these predictions must be supported by
empirical data. In such a case where modeling is used to make and publish detailed
activity predictions, it will create a situation where the given compounds, even the
hypothetical ones, cannot be protected by patents.
Docking is basically just a method to create and score a protein-ligand binding
pose. Indeed, the simplest way to use docking is to estimate a single compound
binding mode like in the work of Lee et al. [16], which utilized docking together with
Molecular Modeling of Protein Kinases: Current Status and Challenges
29