Novel binding patterns between ganoderic acids and neuraminidase: Insights from docking, molecular dynamics and MM/PBSA studies

Journal of Molecular Graphics & Modelling
Zhiwei YangShengli Zhang

Abstract

Recently, ganoderic acids (GAs) give rise to the attractive candidates of novel neuraminidase (NA) inhibitors. However, there is still no evident conclusion about their binding patterns. To this end, docking, molecular dynamics and MM/PBSA methods were combined to study the binding profiles of GAs with the N1 protein and familiar H274Y and N294S mutations (A/Vietnam/1203/04 stain). It was found that the binding affinities of ganoderic acid DM and Z (ΔGbind, -16.83 and -10.99 kcal mol(-1)) are comparable to that of current commercial drug oseltamivir (-23.62 kcal mol(-1)). Electrostatic interaction is the main driving force, and should be one important factor to evaluate the binding quality and rational design of NA inhibitors. The 150-loop residues Asp151 and Arg152 played an important role in the binding processes. Further analysis revealed that ganoderic acid DM is a potential source of anti-influenza ingredient, with novel binding pattern and advantage over oseltamivir. It had steric hindrance on the 150 cavity of N1 protein, and exerted activities across the H274Y and N294S mutations. This work also pointed out how to effectively design dual-site NA inhibitors and reinforce their affinities. These findings should prove valu...Continue Reading

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Citations

Nov 23, 2016·Future Medicinal Chemistry·Zhiwei YangGang Yang
Jan 26, 2018·Frontiers in Molecular Biosciences·Changhao WangRay Luo
Aug 5, 2017·Journal of Biomolecular Structure & Dynamics·Zhiwei YangShengli Zhang
Dec 20, 2017·Apoptosis : an International Journal on Programmed Cell Death·Ting WangLintao Jia
Oct 16, 2019·Journal of Biomolecular Structure & Dynamics·Yongjian ZangShengli Zhang
Jun 6, 2021·Journal of Molecular Graphics & Modelling·Natália Fernandes FrotaMarcos Roberto Lourenzoni

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