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Alzheimer’s disease (AD) is an age-related neurodegenerative disorder. β-amyloid protein (Aβ) is the key protein which involved in AD. But the physiological function of Aβ is needed to be investigated. Many experimental studies have shown that Aβ could bind to glycoproteins D (gD) on the surface of the herpes virus. However the mechanism is still unclear. In the present study, we elucidate the molecular mechanism of the interaction between Aβ and gD of herpes simplex virus type 2 (HSV-2) by molecular docking and molecular dynamics simulation. Molecular dynamics simulations displayed that Aβ could stably bind to the HSV-2 gD owing to the presence of several interactions. Analysis binding free energy by molecular mechanics Poisson–Boltzmann surface area (MM–PBSA) method revealed that hot residues including Glu3, Glu11, Glu22 and Ala42 of Aβ1-42 were involved in binding with HSV-2 gD. Thus, the HSV-2 gD can be entrapped by Aβ which will be utilized for prevent and therapy of AD in future.