Structural insights into the inhibitor binding and new inhibitor design to Polo-like kinase-1 Polo-box domain using computational studies

Journal of Biomolecular Structure & Dynamics
Maaged Abdullah, Lalitha Guruprasad

Abstract

Polo box domain (PBD) from Polo-Like Kinase-1 (PLK-1) a cell cycle regulator is one of the important non-kinase targets implicated in various cancers. The crystal structure of PLK-1 PBD bound to phosphopeptide inhibitor is available and acylthiourea derivatives have been reported as potent PBD inhibitors. In this work, structure and ligand-based pharmacophore methods have been used to identify new PBD inhibitors. The binding of acylthiourea analogs and new inhibitors to PBD were assessed using molecular docking and molecular dynamics simulations to understand their binding interactions, investigate the complex stability and reveal the molecular basis for inhibition. This study provides the binding free energies and residue-wise contributions to decipher the essential interactions in the protein-inhibitor complementarity for complex formation and the design of new PBD inhibitors with better binding. Communicated by Ramaswamy H. Sarma.

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Citations

Feb 20, 2020·Journal of Biomolecular Structure & Dynamics·Gatta K R S Naresh, Lalitha Guruprasad

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Methods Mentioned

BETA
microscale thermophoresis

Software Mentioned

CHARMM
DS
pharmit
MM
PBSA
MODELLER
Chimera UCSF
Antechamber
CDOCKER
mmpbsa

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