Structural insights into inhibition mechanism of the helicase-primase complex from human herpesvirus 1

Human herpesviruses (HHVs) are widespread pathogens causing severe diseases, especially in immunocompromised individuals, and are linked to neurodegenerative and autoimmune disorders. Current antiviral therapies primarily target the α-subfamily, with limited options for β- and γ-subfamilies. The helicase-primase complex (HPC) is essential for viral DNA replication and represents a key antiviral target, but its structure and inhibition mechanisms were previously unclear. Here, cryo-EM structures of the HHV1 (α-subfamily) HPC bound to single-stranded DNA and two clinical inhibitors, amenamevir and pritelivir, are reported. The HPC features flexible helicase and primase modules, with both inhibitors binding a shared allosteric pocket in the helicase module. Structural, biochemical, and molecular dynamics analyses indicate that these inhibitors lock the helicase in an open, inactive conformation. Combined molecular dynamics and fragment molecular orbital analyses explain the α-subfamily selectivity and distinct antiviral spectra of these drugs. These findings provide a structural framework to guide the development of novel inhibitors targeting β- and γ-subfamily herpesviruses.