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Prediction of AChE-ligand affinity using the umbrella sampling simulation.

Ngo Thi Lan1, Khanh B Vu2, Minh Khue Dao Ngoc3

  • 1Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Vietnam.

Journal of Molecular Graphics & Modelling
|September 4, 2019
PubMed
Summary

Acetylcholinesterase inhibitors are crucial for Alzheimer's disease (AD) treatment. Umbrella sampling (US) accurately estimates inhibitor binding affinity to AChE, aiding drug discovery.

Keywords:
ADMEAcetylcholinesteraseBinding affinityCordycepsDockingUmbrella sampling

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Area of Science:

  • Computational chemistry
  • Biochemistry
  • Pharmacology

Background:

  • Alzheimer's disease (AD) poses a significant challenge, with acetylcholinesterase (AChE) identified as a primary therapeutic target.
  • Accurate estimation of ligand-AChE binding affinity is essential for screening potential AD inhibitors.

Purpose of the Study:

  • To evaluate the efficacy of biased sampling, specifically umbrella sampling (US), for estimating AChE-inhibitor binding free energy.
  • To assess the potential of Cordyceps derivatives, particularly 5-Carboxy-2 extquotesingle-deoxyuridine, as AChE inhibitors for AD.

Main Methods:

  • Umbrella sampling (US) simulations were employed to calculate the potential of mean force (PMF) and derive binding free energies.
  • Linear regression analysis was used to determine absolute binding free energies, with root-mean-square errors (RMSE) calculated.
  • In silico ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) properties, including Lipinski's rule of five and blood-brain barrier penetration, were evaluated.

Main Results:

  • US simulations provided reliable estimates of AChE-inhibitor affinity, showing a strong correlation (R=0.94) with experimental values, despite a slight overestimation (∼4.10 kcal/mol).
  • The mean error in free energy estimation was low (δ=1.17 kcal/mol), indicating high precision.
  • 5-Carboxy-2 extquotesingle-deoxyuridine from Cordyceps demonstrated AChE inhibitory activity and favorable pharmacokinetic properties, including BBB permeability.

Conclusions:

  • Umbrella sampling is a robust technique for consistently appraising ligand-AChE binding affinities and discriminating between compounds with similar binding strengths.
  • Cordyceps derivatives, exemplified by 5-Carboxy-2 extquotesingle-deoxyuridine, represent promising candidates for Alzheimer's disease therapy due to their AChE inhibitory potential and drug-like properties.