Molecular modelling and bioinformatics studies of CDK4 and related proteins

Cyclin-dependent kinases play a key role in the regulation of the eukaryotic cell cycle. CDK4 regulates the G1/S phase transition and the entry into the S-phase of the cell cycle. The activity of CDK4 is misregulated in many human cancers. The natural product fascaplysin inhibits CDK4 specifically, and is considered as a lead compound for specific CDK4 inhibitors. In the present work the structural features of the active sites of CDKs are compared, the evolution of CDKs is studied and homology models of CDK4 are generated and used to gain insights into its sequential and structural features. Also the CDK4-ligand interactions of fascaplysin and its tryptamine based derivatives are predicted and the fascaplysin specificity for CDK4 is at least partially explained using thermodynamic integration. CDK4 homology models were generated based on CDK2 templates. However, after the availability of experimentally determined X-ray structures of CDK4 in an inactive form, CDK4 models were built in a putative active form by incorporating the structural information from both CDK4 and CDK2 for its later use in molecular modelling. Docking studies on fascaplysin with CDK4 predict a polar contact between His95CDK4 and fascaplysin in addition to bidentate hydrogen bonds with Val96. This interaction partly explains the selectivity for CDK4 compared to CDK2. The effect of the positive charge of fascaplysin on specificity is studied in thermodynamic integration MD simulations by the isoelectronic substitution of the positively charged nitrogen into a carbon atom. From these thermodynamics integration calculations it is concluded that fascaplysin shows a preference for CDK4 due to better stabilization of the positive charge. ChemScores for tryptamine based derivatives docked into CDK4 show a weak correlation with experimental IC50 values. This indicates that the ChemScores can be used as a weak predictor for relative affinities of CDK4 inhibitors. A new class of α- carboline based inhibitors is proposed, and based on docking studies, predicted to have improved binding affinities for CDK4.