Docking And Molecular Dynamics: Simulation Of The Inhibition Of H5n1 Influenza Virus (Anhui 2005) Neuraminidase (Na) By Chlorogenic Acid (Cha)

Background: Chlorogenic acid (CHA) is an effective component of many traditional Chinese medicines for clearing away heat and detoxification. Studies have shown that CHA can inhibit the influenza virus neuraminidase (NA) and thus exert direct anti-influenza virus action, but the mechanism of inhibition of CHA in NA is not clear. The molecular docking method plays an important role in the study of the mechanism of traditional Chinese medicine active ingredients or natural products against influenza, and provides an effective tool for the discovery and optimization of compounds. Objective: To explore docking and molecular dynamics of the Inhibition of H5N1 Influenza Virus (Anhui 2005) Neuraminidase (NA) by Chlorogenic Acid (CHA). Methods: This study mainly used the molecular docking calculation method to obtain the interaction model between CHA and NA molecules, and then molecular dynamics (MD) simulations were performed to optimize a global 3-D model. The molecular dynamics trajectory data can also be used to calculate the binding free energy between CHA and NA using the MM-PBSA calculation. The key amino acids of the CHA-NA interaction have been analyzed. The mechanism of inhibition of CHA against influenza virus was described from the perspective of structure, energy and amino acid virtual mutation. Results: It was found that as the same as most NA inhibitors, CHA interacted with hydrogen by Arg292, Arg371, Arg118, Glu119 and Glu276 in the surface-active cavity of NA. In addition, CHA also produced a weak interaction with Arg152 of the NA-150-cavity in the form of hydrogen bonds, but did not link with other amino acids of the NA-150-cavity. Conclusion: CHA and NA have non-binding interactions with the traditional surface-active cavity and NA-150-cavity, thereby preventing the flu virus from further invading the host cell. CHA can be an ideal compound, providing broad research prospects for further drug molecular design against the influenza virus NA, especially for the NA-150-cavity.