Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations.

Integrase (IN) is one of the three fundamental enzymes for the HIV life cycle. It irreversibly inserts the viral DNA into the host DNA, infecting the host cells. Although there are 37 compounds currently used in the HIV-1 antiretroviral therapy, only three have IN as a target. Lack of structural and mechanistic information on IN greatly contributes to such a small number. Prototype Foamy Virus (PFV) IN has an enzymatic activity remarkably similar to HIV IN and is considered a model system to study the catalytic mechanism of HIV IN. Recently, the crystal structure of the PFV intasome became available, which allowed us to perform accurate high-level quantum mechanics/molecular mechanics (QM/MM) calculations to determine the strand transfer reaction mechanism followed by IN. We describe here, for the first time with atomic detail, the integration of a viral genome into the DNA of a host cell. We found that the strand transfer reaction mechanism has three distinct steps: deprotonation and activation of the nucleophile; SN2 transesterification involving a pentacoordinated transition state; and protonation of the leaving group. The chemical steps have a limiting potential activation energy of 14.8 kcal/mol at the MPWB1K/6-311++G(2d,2p) level of theory, which is consistent with the upper limit established experimentally (25.1 kcal/mol) associated with the product release. This work improves the mechanistic knowledge on the IN chemistry and provides accurate structures of all the intermediates and transition states, which can be used as templates for the discovery of new IN inhibitors.