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Unbinding free energy of acetylcholinesterase bound oxime drugs along the gorge pathway from metadynamics-umbrella sampling investigation.

Authors
  • Pathak, Arup K
  • Bandyopadhyay, Tusar
Type
Published Article
Journal
Proteins Structure Function and Bioinformatics
Publisher
Wiley (John Wiley & Sons)
Publication Date
Sep 01, 2014
Volume
82
Issue
9
Pages
1799–1818
Identifiers
DOI: 10.1002/prot.24533
PMID: 24549829
Source
Medline
Keywords
License
Unknown

Abstract

Because of the pivotal role that the nerve enzyme, acetylcholinesterase plays in terminating nerve impulses at cholinergic synapses. Its active site, located deep inside a 20 Å gorge, is a vulnerable target of the lethal organophosphorus compounds. Potent reactivators of the intoxicated enzyme are nucleophiles, such as bispyridinium oxime that binds to the peripheral anionic site and the active site of the enzyme through suitable cation-π interactions. Atomic scale molecular dynamics and free energy calculations in explicit water are used to study unbinding pathways of two oxime drugs (Ortho-7 and Obidoxime) from the gorge of the enzyme. The role of enzyme-drug cation-π interactions are explored with the metadynamics simulation. The metadynamics discovered potential of mean force (PMF) of the unbinding events is refined by the umbrella sampling (US) corrections. The bidimensional free energy landscape of the metadynamics runs are further subjected to finite temperature string analysis to obtain the transition tube connecting the minima and bottlenecks of the unbinding pathway. The PMF is also obtained from US simulations using the biasing potential constructed from the transition tube and are found to be consistent with the metadynamics-US corrected results. Although experimental structural data clearly shows analogous coordination of the two drugs inside the gorge in the bound state, the PMF of the drug trafficking along the gorge pathway point, within an equilibrium free energy context, to a multistep process that differs from one another. Routes, milestones and subtlety toward the unbinding pathway of the two oximes at finite temperature are identified.

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