Molecular Simulation Study On The Anti-H5N1 Avian Influenza Virus Effect Of Caffeic Acid(CA)and Chlorogenic Acid(CHA)

Background:Bird flu is a poultry avian infectious disease caused by the avian influenza A virus.In recent years,it has been reported that many people have been infected with the bird flu virus.In all known cases of human bird flu,the symptoms caused by the H5N1 avian influenza virus are the most serious and have the widest distribution.Caffeic acid(CA)and chlorogenic acid(CHA)are active ingredients in many Chinese medicines.Studies have shown that they have a good inhibitory effect on influenza viruses,especially as influenza virus neuraminidase(NA)inhibitors which play an important role in blocking virus replication and transmission;however,the specific binding modes and interactions of caffeic acid,chlorogenic acid with NA protein are not very clear.The main purpose of this paper is to investigate the interaction pattern between neuraminidase and caffeic acid,chlorogenic acid through molecular simulation technology,and to explore the anti-virus mechanism of caffeic acid and chlorogenic acid on influenza virus,and finally to use caffeic acid as the guide compounds of the new anti-influenza virus drug design for a preliminary exploration.Method:1.Homology modeling technology was used to predicte the 3-D structure of neuraminidase of H5N1 avian influenza virus;2.Molecular dynamics(MD) simulation and MM-PBSA binding free energy calculation were explored to screen out the best calculation model for neuraminidase-oseltamivir(NA-OS)drug system under different force fields,different solvent water models and different dielectric constants;3.Molecular docking calculation was performed to study the interaction models of caffeic acid,chlorogenic acid with influenza virus neuraminidase protein,and to identify the key amino acid sites;4.Virtual mutations were used to further discuss the combination of key amino acids on influenza neuraminidase protein with caffeic acid and chlorogenic acid;5.Grow Scaffold calculation was performed to explore drug molecule design for new anti-influenza virus inhibitors using caffeic acid as a lead compound.Result:1.Three templates with the highest amino acid sequence homology with the highly pathogenic avian influenza virus H5N1(Anhui2005)neuraminidase were found in the PDB database,respectively 3CKZ?A(homology 96%),3B7E?A(with(Source 91%)and 3TI4?B(homology 90%).Using the Profile?3D method to evaluate the initial model,the H5N1 neuraminidase(NA)387 amino acids got all verify scores above "0".The overall structure is reasonable.2.The binding free energy was calculated using the gromacs and g?mmpbsa tools under different force field and solvent water models.Compared with the published free energy binding values,the Amber99sb-tip3p-pdie4 calculation model can simulate the correct neuraminidase and the spatial structure of the small-molecule drug was obtained with a free energy value of-74.163±18.178 k J/mol,which is in agreement with the reference value.Thus,Amber99sb-tip3p-pdie4 is recommended as best calculation model for the later study.3.Both caffeic acid(CA)and chlorogenic acid(CHA)form hydrogen bonds through hydrogen donors and receptors with Arg 292,Arg 371,and Glu 119 sites on the NA,and the combining free energy of NA-CA(WT)and NA-CHA(WT)were calculated as-86.429±25.546 is-52.015±19.987 k J/mol respectively,indicating that the binding power of caffeic acid with NA is far stronger than that of chlorogenic acid and oseltamivir with NA.4.Using caffeic acid as a lead compound,the four potential NA inhibitor compounds C5-1,C5-2,C5-3,and C5-4 were designed using the method of fragment growth.The calculated binding free energy with NA were-128.832 ± 22.543,-99.296 ± 26.942,-106.073 ± 23.256 and-88.657 ± 19.646 k J / mol,respectively.Conclusion:CA and CHA can inhibit influenza virus by hydrogen bonding to amino acid Arg292,Arg371 of the influenza virus NA molecule through its similar benzene ring structure to that of OS.The use of CA as a lead compound drug molecule design can provide theoretical support for the development of new anti-influenza virus drugs.The result of theoretical analysis needs to be verified by further experiments.