On August 24^th, 2017, research collaborators of ICST's Laboratory of Molecular Science (Nguyen Minh Tam, Minh Tho Nguyen, Son Tung Ngo) has just published the article of Evaluation of the absolute affinity of neuraminidase inhibitor using steered molecular dynamics simulations on Journal of Molecular Graphics and Modelling. This article is ranked as the topical perspectives.
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The absolute free energy difference of binding (ΔG) between neuraminidase and its inhibitor was evaluated using fast pulling of ligand (FPL) method over steered molecular dynamics (SMD) simulations. The metric was computed through linear interaction approximation. Binding nature was described by free energy differences of electrostatic and van der Waals (vdW) interactions. The finding indicates that vdW metric is dominant over electrostatics in binding process. The computed values are in good agreement with experimental data with a correlation coefficient of R = 0.82 and error of ΔG_exp = 2.2 kcal/mol. The results were observed using Amber 99SB-ILDN force field in comparison with CHARMM27 and GROMOS96 43a1 force fields. Obtained results may stimulate the search for an Influenza therapy.
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Fig. 2. The details of the initial conformation of the neuraminidase versus inhibitor. The zoom is close up view of the binding site including inhibitor.
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