Putative Anti-Cancer Drug Candidate Targeting the 'PLK-1-Polo-Box Domain' by High Throughput Virtual Screening: A Computational Drug Design Study

Crit Rev Eukaryot Gene Expr. 2019;29(3):251-261. doi: 10.1615/CritRevEukaryotGeneExpr.2019028371.

Abstract

Cancer continues to remain a disease of scientific concern. Significant interest in targeting the Polo-Box-Domain (PBD) of Polo-like-kinase-1 (PLK-1) by novel ligands has arisen. The 'cleft' constituted by amino acid residues W414, H538, and K540 is the traditional target of PLK-1-PBD-inhibitors. However, this 'cleft' is merely a small part of the larger 'Y'-shaped cavity present therein. The objective of this study was to discover inhibitors of the PLK-1-PBD precisely directed against its trimodular 'Y'-pocket. High-throughput structure-based virtual screening (SBVS) of more than 5 million ligands against the aforementioned PLK-1 'Y'-pocket was performed. The SBVS hits were successively subjected to pass through various filters: VINA score ranking, toxicity checker, 'Special Criteria'-filtration, holistic tri-modular 'Y'-pocket interaction check, drug-likeness filters, and medicinal chemistry filters. Accordingly, we arrived at a single top ligand, 'SHAZ-i.' The top ligand, 3-{2-[(2-Methyl-2-propanyl)sulfonyl]phenyl}-5-phenyl-1,2-oxazole-4-carboxamide, displayed a robust interaction with the target crevice through 15 amino acid residues, an acceptable ΔG value of -7.8 kcal/mol, and a favorable pharmacokinetic profile with no adverse effects on humans. Hence, 3-{2-[(2-Methyl-2-propanyl)sulfonyl]phenyl}-5-phenyl-1,2-oxazole-4-carboxamide could emerge as a potent PLK-1-PBD inhibitor or might act as a 'seed' molecule for design of future inhibitors with a closely related backbone structure.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antineoplastic Agents / chemistry
  • Antineoplastic Agents / pharmacology*
  • Cell Cycle Proteins / antagonists & inhibitors*
  • Computational Biology / methods
  • Drug Design*
  • High-Throughput Screening Assays / methods*
  • Humans
  • Neoplasms / drug therapy*
  • Neoplasms / pathology
  • Polo-Like Kinase 1
  • Protein Domains
  • Protein Kinase Inhibitors / chemistry
  • Protein Kinase Inhibitors / pharmacology*
  • Protein Serine-Threonine Kinases / antagonists & inhibitors*
  • Proto-Oncogene Proteins / antagonists & inhibitors*
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology*

Substances

  • Antineoplastic Agents
  • Cell Cycle Proteins
  • Protein Kinase Inhibitors
  • Proto-Oncogene Proteins
  • Small Molecule Libraries
  • Protein Serine-Threonine Kinases