Mechanism of Drug Resistance Revealed by the Crystal Structure of the Unliganded HIV-1 Protease with F53L Mutation

Mutations in HIV-1 protease (PR) that produce resistance to antiviral PR inhibitors are a major problem in AIDS therapy. The mutation F53L arising from antiretroviral therapy was introduced into the flexible flap region of the wild-type PR to study its effect and potential role in developing drug resistance. Compared to wild-type PR, PRF53L showed lower (15%) catalytic efficiency, 20-fold weaker inhibition by the clinical drug indinavir, and reduced dimer stability, while the inhibition constants of two peptide analog inhibitors were slightly lower than those for PR. The crystal structure of PRF53L was determined in the unliganded form at 1.35 Å resolution in space group P41212. The tips of the flaps in PRF53L had a wider separation than in unliganded wild-type PR, probably due to the absence of hydrophobic interactions of the side-chains of Phe53 and Ile50′. The changes in interactions between the flaps agreed with the reduced stability of PRF53L relative to wild-type PR. The altered flap interactions in the unliganded form of PRF53L suggest a distinct mechanism for drug resistance, which has not been observed in other common drug-resistant mutants.