Investigation on the Binding Properties of N1 Neuraminidase of H5N1 Influenza Virus in Complex with Fluorinated Sialic Acid Analog Compounds—a Study by Molecular Docking and Molecular Dynamics Simulations

Worldwide, only two types of antiviral inhibitors (M2 ion channel protein inhibitor and Neuraminidase inhibitors) are approved to treat the influenza viral infection. But mutation amino acid sequence in membrane proteins creates resistance existing drugs or inhibitors. So corresponding have be reformulated match these antigenic variations. Fluorination on carbon–based molecule significantly enriches its biological properties. Hence this study is motivated design fluorinated sialic (SIA) analog for neuraminidase H5N1 A virus by substituting fluorine atom at different hydroxyls (O2, O4, O7, O8, O9) acid. 100 ns molecular dynamics simulations carried out each protein–ligand complex system. NAMD pair interaction energy MM–PBSA binding free calculations predict possible modes N1–SIA_F2, N1–SIA_F4, N1–SIA_F7 complexes single mode N1–SIA_F8 N1–SIA_F9 complexes. RMSD, RMSF, hydrogen bonding analyses used understand conformational flexibility structural stability It has been concluded that drug candidates SIA_F2 SIA_F7 better inhibiting potency against N1 virus.