Binding Mechanism of Inhibitors to CDK5/p25 Complex: Free Energy Calculation and Ranking Aggregation Analysis

Cyclin-dependent kinase-5 (CDK5) plays an indispensable role in the central nervous system. Competitive inhibition of the ATP-binding pocket of CDK5 is involved in fighting with neurodegenerative diseases, diabetes, tumors, inflammations etc. To better design ATP-binding competitive inhibitors, the binding mechanism of three important inhibitors of kinases, (R)-roscovitine (RRC), aloisine-A (ALH) and indirubin-3'-oxime (IXM), together with their receptor CDK5, were studied by molecular dynamics simulations. The H-bond analysis demonstrated that a strong bond was formed between the CO or NH groups in the backbone of Cys83 and the N or NH groups on the nitrogen-containing ring of inhibitors. These hydrogen bonds significantly increase the binding and inhibitory efficiency. The free energy analysis show that the order of predicted binding affinities of these three inhibitors toward CDK5/p25 is IXM>ALH>RRC, which is consistent with the experimental data. Besides the hydrogen bond formation, the van der Waals interactions between residues Ile10, Val18, and Leu133 of CDK5 and inhibitors were discovered to constitute another substantial component of their binding mode. Worth mentioning is that the conformational turnover of the inhibitor RRC was observed during the course of molecular dynamics simulations. We believe that this is the reason why RRC has the lower H-bond occupancy and binding affinity than the other two inhibitors. Furthermore, during the analysis of the per-residue decomposition, the ranking aggregation method was firstly employed to rank the contribution of different residues. The results demonstrated that the top five residues in the active pocket of CDK5 were Cys83, Leu133, Ile10, Phe82, and Glu81, which is in good agreement with the results of H-bond analysis and binding free energy analysis. These findings should provide insights into the inhibition mechanism of the CDK5/p25 complex and be useful for the rational design of novel ATP-binding competitive inhibitors in the near future.