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

Abstract

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.

Multiscale modeling of enzymes: QM‐cluster, QM/MM, and QM/MM/MD: A tutorial review

“…During recent years, Ramos and coworkers have investigated the reaction mechanisms of a large number of enzymes by employing mostly the B3LYP and M06 functionals with/out dispersion corrections in hybrid QM/MM methods . Here, we focus our attention on some of their works in which several density functionals and/or basis sets were tested, to see how they affect the accuracy of the properties such as activation barriers and reaction energies.…”

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

“…We choose to discuss in this section two enzymatic mechanisms, among several studies that we have published in recent years, and several other excellent ones that can be found in literature …”

“…We choose to discuss in this section two enzymatic mechanisms, among several studies that we have published in recent years 112,115,147,149,157,[166][167][168][169][170][171] , and several other excellent ones that can be found in literature. [150][151][152][153][154] HIV-1 Integrase HIV-1 integrase is part of a set of three fundamental enzymes that are crucial for the life cycle of the HIV virus.…”

The mouse mammary tumor virus intasome exhibits distinct dynamics on target DNA

“…Importantly, calcium cations are essential for the assembly of stable intasomes because they stabilize the IN-vDNA interaction but are incapable of acting as a cofactor during strand transfer (8,46). These calcium cations must be displaced by magnesium or manganese that can serve as metal ion cofactors capable of coordinating the SN2 nucleophilic integration reaction (58). We noted a significant increase in bulk integration products in the presence of the manganese cation (Figure 1).…”