Structure-Based Virtual Screening, Molecular Dynamics and Binding Free Energy Calculations of Hit Candidates as ALK-5 Inhibitors

Molecules. 2020 Jan 9;25(2):264. doi: 10.3390/molecules25020264.

Abstract

Activin-like kinase 5 (ALK-5) is involved in the physiopathology of several conditions, such as pancreatic carcinoma, cervical cancer and liver hepatoma. Cellular events that are landmarks of tumorigenesis, such as loss of cell polarity and acquisition of motile properties and mesenchymal phenotype, are associated to deregulated ALK-5 signaling. ALK-5 inhibitors, such as SB505154, GW6604, SD208, and LY2157299, have recently been reported to inhibit ALK-5 autophosphorylation and induce the transcription of matrix genes. Due to their ability to impair cell migration, invasion and metastasis, ALK-5 inhibitors have been explored as worthwhile hits as anticancer agents. This work reports the development of a structure-based virtual screening (SBVS) protocol aimed to prospect promising hits for further studies as novel ALK-5 inhibitors. From a lead-like subset of purchasable compounds, five molecules were identified as putative ALK-5 inhibitors. In addition, molecular dynamics and binding free energy calculations combined with pharmacokinetics and toxicity profiling demonstrated the suitability of these compounds to be further investigated as novel ALK-5 inhibitors.

Keywords: ALK-5; SBVS; binding free energy calculations; cancer; molecular dynamics.

MeSH terms

  • Antineoplastic Agents / chemistry*
  • Antineoplastic Agents / isolation & purification
  • Antineoplastic Agents / pharmacology
  • Binding Sites
  • Humans
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Protein Binding / drug effects
  • Protein Conformation / drug effects*
  • Protein Kinase Inhibitors / chemistry*
  • Protein Kinase Inhibitors / isolation & purification
  • Protein Kinase Inhibitors / pharmacology
  • Pyrazoles / chemistry
  • Quinolines / chemistry
  • Receptor, Transforming Growth Factor-beta Type I / antagonists & inhibitors
  • Receptor, Transforming Growth Factor-beta Type I / chemistry*
  • Receptor, Transforming Growth Factor-beta Type I / ultrastructure
  • User-Computer Interface

Substances

  • Antineoplastic Agents
  • Protein Kinase Inhibitors
  • Pyrazoles
  • Quinolines
  • LY-2157299
  • Receptor, Transforming Growth Factor-beta Type I
  • TGFBR1 protein, human