Evaluating the antiviral potential of Thymus vulgaris constituents and curcumin against influenza hemagglutinin: A molecular dynamics study

This study used molecular modelling to investigate how phytochemicals from Thymus vulgaris ( T. vulgaris ) and curcumin modulate the conformational stability of the influenza virus hemagglutinin (HA) protein. Drug-likeness screening showed that the T. vulgaris constituents thymol, linalool and carvacrol comply with Lipinski's Rule of Five, supporting their potential as orally available lead compounds. All-atom molecular dynamics simulations were then performed to characterize their interactions with HA, and electrostatic and Lennard–Jones interaction energy components between HA and each ligand were extracted along the trajectories. The T. vulgaris compounds displayed more favorable binding energies with HA than curcumin. It is indicated that linalool, thymol and carvacrol have been adsorbed on receptor binding sites and fusion related stalk of HA . Secondary-structure analysis further showed a ligand-dependent increase in disordered coil content accompanied by a reduction in β-sheet elements in HA in the presence of T. vulgaris phytochemicals. Taken together, these results indicate that T. vulgaris components can stably associate with HA and promote conformational changes that are consistent with functional inactivation, suggesting that they are promising phytochemical scaffolds for the rational design of herbal-derived anti-influenza agents.