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Benzimidazole inhibitors of the protein kinase CHK2: clarification of the binding mode by flexible side chain docking and protein-ligand crystallography.
(2012) Bioorg Med Chem 20
PubMed: 23058106 | PubMedCentral: PMC3778940 | DOI: 10.1016/j.bmc.2012.09.024
49 4.3 Protein crystal structure preparation CHK2 crystal structures (PDB ID: 2CN5 and 2W0J) representing different ligand binding modes were obtained from the Protein databank.
Figure 2 Binding of (A) ADP to CHK2 (PDB ID: 2CN5 ) 42 and (B) NSC109555 to CHK2 (PDB ID: 2W0J ).
15–17 We chose the structures of CHK2 bound to ADP (PDB ID: 2CN5 ) and to NSC1095555 (PDB ID: 2W0J ) as representative high resolution parent structures for docking [2.25 and 2.05 Å, respectively].
Ligands which docked via the mediating water molecule to the apo-structure derived from the NSC-109555-bound structure (PDB ID: 2W0J ).
Figure 6 Overlay of the flexible residues in the binding sites of the NSC109555-bound crystal structure (green, PDB ID: 2W0J ) and ligand 30 -induced protein structure (purple).
In summary, an unconstrained rigid docking protocol yielded a higher hit rate when applied to the NSC109555-derived protein structure 2W0J versus the ADP-derived protein structure 2CN5; however, neither protein structure provides binding mode solutions consistent with the importance of interactions from all 4 polar atoms of the benzimidazole–carboxamide scaffold, as demonstrated by the experimental SAR ( vide supra and Table 1 ).
Shown is (A), the CHK2 binding site highlighting residues which adopt a different conformation in the ligand 30 -induced protein structure (purple) and (B), a cut away depiction highlighting residues which adopt a different conformation in the ligand 30 -induced protein structure (purple) versus the parent crystal structure (green, PDB ID: 2W0J ); arrows indicate side chains that have changed conformation significantly.
In brief, we first applied a distance cut-off, based upon our rigid docking results for protein structures 2CN5 and 2W0J, to include all protein residues of the respective ligand-binding site with the potential to be treated as flexible.
Application of these criteria reduced the number of selected residues to 16 and 27 in the 2CN5 and 2W0J structures, respectively ( Table S2, Supplementary data ).
The search space was defined by locating the centre of the ligand present in each crystal structure (ADP for structure 2CN5 and NSC109555 for structure 2W0J) and using a radius of 16 Å from the centroid to define the volume of the binding pocket searched during docking.
15–17 We compared the optimal ligand 30 -induced conformation with the crystal structure 2W0J ( Fig. 6 ).
2.3 Flexible docking of benzimidazole inhibitors We hypothesised that rigid docking may preclude the optimal orientation of protein side chains in the ATP binding site and applied a docking protocol incorporating side chain flexibility to both binding modes of CHK2 exemplified by protein structures 2W0J and 2CN5.
Of the 10 residues treated as flexible, all hydrophobic protein side chains are aligned similarly in both the ligand 30 -induced conformation and in 2W0J.
Publication Year: 2012
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