Exploring the Binding Nature of Pyrrolidine Pocket-Dependent Interactions in the Polo-Box Domain of Polo-Like Kinase 1

Abstract

BackgroundOver the years, a great deal of effort has been focused on the design and synthesis of potent, linear peptide inhibitors targeting the polo-like kinase 1 (Plk1), which is critically involved in multiple mitotic processes and has been established as an adverse prognostic marker for tumor patients. Plk1 localizes to its intracellular anchoring sites via its polo-box domain, and inhibiting the Plk1 polo-box domain has been considered as an approach to circumvent the specificity problems associated with inhibiting the conserved adenosine triphosphate-binding pocket. The polo-box domain consists of two different binding regions, such as the unique, broader pyrrolidine-binding pocket and the conserved, narrow, Tyr-rich hydrophobic channel, among the three Plk polo-box domains (Plks 1–3), respectively. Therefore, the studies that provide insights into the binding nature of the unique, broader pyrrolidine-binding pocket might lead to the development of selective Plk1-inhibitory compounds.Methodology/Principal FindingsIn an attempt to retain the monospecificity by targeting the unique, broader pyrrolidine-binding pocket, here, for the first time, a systematic approach was undertaken to examine the structure-activity relationship of N-terminal-truncated PLHSpTM derivatives, to apply a site-directed ligand approach using bulky aromatic and non-aromatic systems, and to characterize the binding nature of these analogues using X-ray crystallographic studies. We have identified a new mode of binding interactions, having improved binding affinity and retaining the Plk1 polo-box domain specificity, at the pyrrolidine-binding pocket. Furthermore, our data revealed that the pyrrolidine-binding pocket was very specific to recognize a short and bulky hydrophobic ligand like adamantane, whereas the Tyr-rich hydrophobic channel was specific with lengthy and small hydrophobic groups.Conclusion/SignificanceThe progress made using our site-directed ligands validated this approach to specifically direct the ligand into the unique pyrrolidine-binding region, and it extends the applicability of the strategy for discovering selective protein-protein interaction inhibitors.

Recent Advances and New Strategies in Targeting Plk1 for Anticancer Therapy

“…However, significant loss of binding affinity is incurred by shortening the PLHSpT sequence to HSpT, indicating that interactions provided by the amino-terminal region of the peptide are also important [82]. Optimization of the N -terminal interactions has been attempted to improve the affinity of the parent sequence by introducing bulky hydrophobic groups into the N -terminal Pro residue [138]. …”

Structural analysis of the polo‐box domain of human Polo‐like kinase 2

“…(B)]. Second, the PB1‐PB2 loop is usually disordered in part or entirely in the structures of Plk1‐PBD . However, in the crystal structure we identified, both the loops from Plk2‐PBD and Plk2‐PBD′ are ordered well (Supporting Information Fig.…”

“…This dimerization is yet questionable because the PBD of Plk1 (referred to as Plk1‐PBD), sharing 33% sequence identity and 54% similarity with Plk2‐PBD based on the structure‐based sequence alignment (Supporting Information Fig. S3), has been reported as a monomer in a number of previous structural studies . To investigate this issue, SEC‐MALS was performed, which is a powerful tool for determining the molecular weight of macromolecules in solution.…”

Pyrrole‐Based Macrocyclic Small‐Molecule Inhibitors That Target Oocyte Maturation

“…Macrocyclic compounds were injected into oocytes by means of an Eppendorf Femto Jet (Eppendorf AG, Hamburg, Germany) and aN ikon Diaphot ECLIPSE TE300 inverted microscope (Nikon UK Ltd.,K ingston upon Thames, Surrey,U K) equipped with aN arishige MM0-202N hydraulic three-dimensional micromanipulator (Narishige Inc.,S ea Cliff,N Y, USA) and subjected to in vitro maturation as described above. As ac ontrol, the Bg34 reagent [9] with threonine residues instead of phosphothreonine was injected into oocytes at 300 mm. ChemMedChem 2017, 12,580 -589 www.chemmedchem.org…”

“…The present work emergeda sp art of ar esearch program that recently embarked on the development of oocytem aturation blockings tudies [4] and PLK1 PBD inhibitor synthesis. [8][9][10][11] In this work, we have designed and synthesized an N-phenylalkyl pyrrole-based macrocyclic inhibitor featuring phosphate residues on the alkyl side chain. To mimicA B103-8, we closelye xamined its binding in the crystal structure of PLK1 PBD in complex with compound 702 (PDB ID:5 DMJ).…”