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

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

Keywords:

• Polo-like kinase-1 Polo-box domain
• PLHSpT phosphopeptide
• pharmacophore-based virtual screening
• molecular docking
• molecular dynamics simulations

Acknowledgments

The authors thank CMSD, University of Hyderabad for providing computational facilities. MA thanks Ministry of Higher Education & Scientific Research, Republic of Yemen.

Disclosure statement

No potential conflict of interest was reported by the authors.