Peramivir is developed by structure-based drug design. After the influenza NA inhibitor activity of α/β-6-acetyl-amino-3,6-dideoxy -D-glycero-altro-2-nonulofuranosonic acid was reported by Yamamoto et al., the cyclopentane derivatives was designed with a guanidino group replacing C4-hydroxyl position of DANA in the active site, similar to Zanamivir. Babu et al. found that the addition of n-butyl side chain makes the compound fit better to the hydrophobic region of the enzyme. However, the conformation of the n-butyl group was found to be different when bound to influenza virus A from its conformation when bound to influenza virus B.
 Since the compound processed similar binding interaction with active site of NA to zanamivir and due to the mutation in some zanamivir-resistance strains, the position of guanidino group was altered and the n-butyl group was replaced in order to change its active site interaction.