Yuan-Hua Ding

Selectivity-determining residues in Plk1.

Polo‐like kinase 1 is an important regulator of cell cycle progression whose over‐expression is often associated with oncogenesis. Polo‐like kinase 1 hence represents an attractive target for cancer intervention. BI 2536 (Boehringer Ingelheim, Ingelheim, Germany), a Polo‐like kinase 1 inhibitor currently in clinical trials, exhibits nanomolar potency against Polo‐like kinase isoforms and high selectivity against other kinases. We have previously published the crystal structures of the Polo‐like kinase 1 domain in complex with AMPPNP and an Aurora A inhibitor. In this work, we present the co‐crystal structure of Polo‐like kinase 1 with BI 2536. The structure, in combination with selectivity data for BI 2536 and related compounds, illustrates important features for potency and selectivity. In particular, we show that the methoxy group of BI 2536 is an important specificity determinant against non‐Polo‐like kinases by taking advantage of a small pocket generated by Leu 132 in the hinge region of Polo‐like kinase 1. The work presented here provides a framework for structure‐based drug design of Polo‐like kinase 1‐specific inhibitors.

Identification of Allosteric PIF-Pocket Ligands for PDK1 using NMR-Based Fragment Screening and 1H-15N TROSY Experiments

Aberrant activation of the phosphoinositide 3‐kinase pathway because of genetic mutations of essential signalling proteins has been associated with human diseases including cancer and diabetes. The pivotal role of 3‐phosphoinositide‐dependent kinase‐1 in the PI3K signalling cascade has made it an attractive target for therapeutic intervention. The N‐terminal lobe of the 3‐phosphoinositide‐dependent kinase‐1 catalytic domain contains a docking site which recognizes the non‐catalytic C‐terminal hydrophobic motifs of certain substrate kinases. The binding of substrate in this so‐called PDK1 Interacting Fragment pocket allows interaction with 3‐phosphoinositide‐dependent kinase‐1 and enhanced phosphorylation of downstream kinases. NMR spectroscopy was used to a screen 3‐phosphoinositide‐dependent kinase‐1 domain construct against a library of chemically diverse fragments in order to identify small, ligand‐efficient fragments that might interact at either the ATP site or the allosteric PDK1 Interacting Fragment pocket. While majority of the fragment hits were determined to be ATP‐site binders, several fragments appeared to interact with the PDK1 Interacting Fragment pocket. Ligand‐induced changes in 1H‐15N TROSY spectra acquired using uniformly 15N‐enriched PDK1 provided evidence to distinguish ATP‐site from PDK1 Interacting Fragment‐site binding. Caliper assay data and 19F NMR assay data on the PDK1 Interacting Fragment pocket fragments and structurally related compounds identified them as potential allosteric activators of PDK1 function.

Beyond the MEK-pocket: can current MEK kinase inhibitors be utilized to synthesize novel type III NCKIs? Does the MEK-pocket exist in kinases other than MEK?

An approach and preliminary results for utilizing legacy MEK inhibitors as templates for a reiterative structural based design and synthesis of novel, type III NCKIs (non-classical kinase inhibitors) is described. Evidence is provided that the MEK-pocket or pockets closely related to it may exist in kinases other than MEK.

The Design, Synthesis and Potential Utility of Fluorescence Probes that Target DFG-out Conformation of p38alpha for High Throughput Screening Binding Assay.

The design, synthesis and utility of fluorescence probes that bind to the DFG‐out conformation of p38α kinase are described. Probes that demonstrate good affinity for p38α, have been identified and one of the probes, PF‐04438255, has been successfully used in an high throughput screening (HTS) assay to identify two novel non‐classical p38α inhibitors. In addition, a cascade activity assay was utilized to validate the selective binding of these non‐classical kinase inhibitors to the unactive form of the enzyme.

Selectivity-determining Residues in Plk1: Selectivity-determining Residues in Plk1

Polo‐like kinase 1 is an important regulator of cell cycle progression whose over‐expression is often associated with oncogenesis. Polo‐like kinase 1 hence represents an attractive target for cancer intervention. BI 2536 (Boehringer Ingelheim, Ingelheim, Germany), a Polo‐like kinase 1 inhibitor currently in clinical trials, exhibits nanomolar potency against Polo‐like kinase isoforms and high selectivity against other kinases. We have previously published the crystal structures of the Polo‐like kinase 1 domain in complex with AMPPNP and an Aurora A inhibitor. In this work, we present the co‐crystal structure of Polo‐like kinase 1 with BI 2536. The structure, in combination with selectivity data for BI 2536 and related compounds, illustrates important features for potency and selectivity. In particular, we show that the methoxy group of BI 2536 is an important specificity determinant against non‐Polo‐like kinases by taking advantage of a small pocket generated by Leu 132 in the hinge region of Polo‐like kinase 1. The work presented here provides a framework for structure‐based drug design of Polo‐like kinase 1‐specific inhibitors.

Research Article: Selectivity-determining Residues in Plk1

Polo‐like kinase 1 is an important regulator of cell cycle progression whose over‐expression is often associated with oncogenesis. Polo‐like kinase 1 hence represents an attractive target for cancer intervention. BI 2536 (Boehringer Ingelheim, Ingelheim, Germany), a Polo‐like kinase 1 inhibitor currently in clinical trials, exhibits nanomolar potency against Polo‐like kinase isoforms and high selectivity against other kinases. We have previously published the crystal structures of the Polo‐like kinase 1 domain in complex with AMPPNP and an Aurora A inhibitor. In this work, we present the co‐crystal structure of Polo‐like kinase 1 with BI 2536. The structure, in combination with selectivity data for BI 2536 and related compounds, illustrates important features for potency and selectivity. In particular, we show that the methoxy group of BI 2536 is an important specificity determinant against non‐Polo‐like kinases by taking advantage of a small pocket generated by Leu 132 in the hinge region of Polo‐like kinase 1. The work presented here provides a framework for structure‐based drug design of Polo‐like kinase 1‐specific inhibitors.