On the Origins of Enzyme Inhibitor Selectivity and Promiscuity: A Case Study of Protein Kinase Binding to Staurosporine

Abstract

Relationships between ligand binding and the shapes of the binding sites in families of homologous enzymes are investigated by comparing matrices of distances between key binding site atoms. Multiple linear regression is used to help identify key distances that influence ligand binding affinity. In order to illustrate the utility of this generic approach, we study protein kinase binding sites for ATP and the promiscuous competitive inhibitor, staurosporine. We show that the size of the gatekeeper residue and the closure between the first glycine of the GXGXXG motif and the aspartate of the DFG loop act together to promote tight binding. Our web-based tool, ‘mapping analogous hetero-atoms onto residue interactions’ (MAHORI), indicates that the greater the number of hydrogen bonds made by the kinase around the methylamine group of staurosporine, the tighter the binding. The conservation of surrounding atoms identified using our novel grid-based method clearly demonstrates that the most structurally conserved part of the binding site for staurosporine is the main chain of the hinge region. The critical role of interactions that are not dependent on side-chain identities is consistent with the promiscuous nature of this inhibitor.

CDK Inhibitors Roscovitine and CR8 Trigger Mcl-1 Down-Regulation and Apoptotic Cell Death in Neuroblastoma Cells

“…22,29,44 To examine whether interaction with any of these targets might account for the induction of Mcl-1 down-regulation by roscovitine or CR8, we made use of a series of selective pharmacological inhibitors of these kinases (none of these inhibit CDKs) ( Figure 4 49 ). In contrast to a general kinase inhibitor (staurosporine 50 ), roscovitine, and CR8, none of these inhibitors induced Mcl-1 down-regulation. N6-methyl-roscovitine, a kinase inactive derivative of roscovitine, 51 was unable to trigger Mcl-1 down-regulation.…”

Structural and functional restraints in the evolution of protein families and superfamilies

“…However, amino acids some distance away can also be under restraint, particularly from the need to maintain precise arrangements of catalytic residues and cofactor-binding interactions. Conversely, amino acid substitutions may affect substrateand drug-binding specificity, a factor evident in the analysis of kinase drugs (Figure 4) [29].…”

Generation and Characterization of ATP Analog-specific Protein Kinase Cδ

“…Mutation of the gatekeeper residue usually causes minimal change in kinase activity (47) but might confer resistance to inhibitors. The size of the gatekeeper residue has been correlated with the binding affinity for staurosporine (51). The group of kinases with larger gatekeeper residues (e.g.…”