Insights into Binding Affinity of Flavonoid Compounds from Thai Herbs against 2009 H1N1 Hemagglutinin

Abstract

Outbreak of influenza virus is one of serious concerns for public health. Hemagglutinin (HA), a spike-shaped glycoprotein on the viral surface, plays an important role during the early stage of influenza infection. In the present work, a set of flavonoids were screened against 2009 H1N1 HA by computational chemistry techniques. Among 35 flavonoids, the docking results showed that the epicatechin gallate (ECG) and puerarin exhibited a good binding affinity towards 2009 H1N1 HA. These 2 compounds were then studied by all-atom molecular dynamics (MD) simulations. The predicted binding free energy of the H1-puerarin complex (–25.86 ± 2.92 kcal/mol) was slightly greater than that of H1-ECG (–22.81 ± 2.19 kcal/mol), suggesting that the puerarin and ECG could provide similar binding affinity towards 2009 H1 HA target. However, the stronger electrostatic energy contribution of ~10 kcal/mol was found in the puerarin binding to 2009 H1N1 HA. This molecular information of ligand-protein interaction could be helpful in further drug design and development for influenza treatment.
 HIGHLIGHTS
 
 The 35 flavonoid bioactive compounds were screened against 2009 H1N1 HA by molecular docking
 The epicatechin gallate (ECG) and puerarin exhibited a good binding affinity and were then studied by all-atom molecular dynamics (MD) simulations
 The predicted binding free energy revealed that the puerarin and ECG could provide similar binding affinity towards 2009 H1 HA target
 
 GRAPHICAL ABSTRACT