Evaluation of the absolute affinity of neuraminidase inhibitor using steered molecular dynamics simulations
Nguyen Minh Tam1, Minh Tho Nguyen2, Son Tung Ngo1
1Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
Abstract:
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 σΔGexp=2.2kcal/mol. The results were observed using Amber99SB-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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