Determining the Relative Binding Affinity of Ricin Toxin A Inhibitors by Using Molecular Docking and Nonequilibrium Work

J Chem Inf Model. 2018 Jun 25;58(6):1205-1213. doi: 10.1021/acs.jcim.8b00036. Epub 2018 May 25.

Abstract

Ricin is a ribosome-inactivating protein (RIP type 2) consisting of two subunits, ricin toxin A (RTA) and ricin toxin B (RTB). Because of its cytotoxicity, ricin has worried world authorities for its potential use as a chemical weapon; therefore, its inhibition is of great biotechnological interest. RTA is the target for inhibitor synthesis, and pterin derivatives are promising candidates to inhibit it. In this study, we used a combination of the molecular docking approach and fast steered molecular dynamics (SMD) to assess the correlation between nonequilibrium work, ⟨ W⟩, and the IC50 for six RTA inhibitors. The results showed that molecular docking is a powerful tool to predict good bioactive poses of RTA inhibitors, and ⟨ W⟩ presented a strong correlation with IC50 ( R2 = 0.961). Such a profile ranked the RTA inhibitors better than the molecular docking approach. Therefore, the combination of docking and fast SMD simulation was shown to be a promising tool to distinguish RTA-active inhibitors from inactive ones and could be used as postdocking filtering approach.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antitoxins / chemistry*
  • Antitoxins / pharmacology*
  • Chemical Warfare Agents / chemistry
  • Chemical Warfare Agents / metabolism
  • Humans
  • Ligands
  • Molecular Docking Simulation
  • Pterins / chemistry*
  • Pterins / pharmacology*
  • Ricin / antagonists & inhibitors*
  • Ricin / chemistry
  • Ricin / metabolism*
  • Ricinus / chemistry

Substances

  • Antitoxins
  • Chemical Warfare Agents
  • Ligands
  • Pterins
  • Ricin